Article

Current genetic isolation and fragmentation contrasts with historical connectivity in an alpine lizard (Cyclodomorphus praealtus) threatened by climate change

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  • Arthur Rylah Institute for Environmental Research
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Abstract

Assessing levels of genetic diversity, connectivity and historical demography for threatened species provides important information for conservation management. We used a combination of the mitochondrial ND4 gene and seven microsatellite markers to examine both historical and recent population genetic structure and demography of the threatened alpine she-oak skink, Cyclodomorphus praealtus. This species is restricted to the “sky islands” of the Australian alpine region. Based on mtDNA, the New South Wales and Victorian regions are reciprocally monophyletic and highly divergent, with among population variation of 0.9 and net sequence divergence of 4.28%, which suggests that they should be considered separate Evolutionary Significant Units for management purposes. The mtDNA data also indicate historical connectivity between the three Victorian populations. However, a model-based clustering analysis of microsatellite genotypes identified strong population structure in Victoria, with three distinct populations that have no current inter-population gene flow. This suggests that the Victorian populations are effectively isolated from each other, and is indicative of very low dispersal capacity and a high degree of habitat specialisation. This is reinforced by the substantially lower genetic diversity within the lowest elevation population compared to the other higher elevation populations. We found no genetic signature of major changes in effective population size. These data provide a baseline for assessing future impacts of climate change on the genetic structure of this alpine endemic species.

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... Many threatened animal species are elusive and difficult to observe in the wild (Durso et al. 2011). Obtaining information on such species' population demographics can therefore present a significant challenge (Koumoundouros et al. 2009). Genetic methods are increasingly used in support of conventional field-based methods to contribute to our understanding of how species respond to environmental change (Koumoundouros et al. 2009;Keely et al. 2014;Stevens et al. 2018). ...
... Obtaining information on such species' population demographics can therefore present a significant challenge (Koumoundouros et al. 2009). Genetic methods are increasingly used in support of conventional field-based methods to contribute to our understanding of how species respond to environmental change (Koumoundouros et al. 2009;Keely et al. 2014;Stevens et al. 2018). Although they come with their own limitations (Bohonak 1999), such methods are invaluable in the study and conservation of threatened species. ...
... To infer the approximate timing for divergences, we used the conventional mtDNA clock calibration of 1.6% sequence divergence per million years (Myr) (Morando et al. 2003), as used in other squamate reptile studies (Chapple et al. 2005;Koumoundouros et al. 2009). Model-corrected genetic divergence was calculated in MEGA6 (Tamura et al. 2013), using 1000 bootstrap (BS) replicates for likelihood estimation. ...
Article
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Understanding the demographic consequences of habitat loss on populations is essential for the conservation of threatened species. The threatened swamp skink (Lissolepis coventryi) is restricted to fragmented wetland habitats in Victoria and southeast South Australia. It has experienced significant habitat loss in the last 150 years, particularly around the Melbourne metropolitan area, where several small and isolated populations remain. Using mtDNA and nuDNA SNPs, we examined distribution patterns and population structure to infer evolutionary history and genetic distinctiveness of populations throughout the species’ range. For populations in the Melbourne metropolitan area, we examined genetic diversity. We found the species to be highly divergent, separating into two distinct lineages to the east and west of Melbourne, likely due to geological and climate influences causing isolation of populations. Species’ detectability was low, particularly in the far east despite relatively intact habitat and presumed higher abundance. Melbourne populations showed signs of limited genetic diversity. We suggest that translocations to promote gene diversity amongst these populations, together with habitat restoration and protection, present an important management strategy for L. coventryi.
... Se encuentra enrollado en un cromosoma circular y en animales está compuesto por 37 genes (Taanman, 1999). Es heredado vía materna, por lo que no se modifica por procesos de recombinación, siendo susceptible a los eventos de deriva génica, y evoluciona bajo el modelo de neutralidad al intervenir en funciones metabólicas básicas de óxido-reducción (Brown et al., 1979;Wan et al., 2004;Koumoundouros et al., 2009;Botham y Mayers, 2010). ...
... Anolis (Arroyo, 2008;Koumoundouros et al., 2009;Vargas y Moreno 2014). ...
... Este resultado es consistente con la mayor distancia geográfica que hay entre estos fragmentos. Está comprobado que la interrupción del flujo genético en poblaciones de lagartijas puede generar diferenciación genética (Semple et al., 2010;Hurtson et al., 2009;Koumoundouros et al., 2009;Lin et al., 2010;Vargas y Moreno, 2014;Sugawara et al., 2015;Vandergast et al., 2016). ...
... In habitat specialist montane species with characteristically poor dispersal ability (McCain & Colwell, 2011), this current isolation inhibits migration and gene flow, promoting inbreeding and genetic drift (Sumner, 2005;Haines et al., 2017). Consequently, this homogenizes genetic diversity within sky-islands (Browne & Ferree, 2007), while producing genetic structure among islands (Mitrovski et al., 2007), increasing rates of both diversification and extinction (Hedrick & Kalinowski, 2000;Koumoundouros et al., 2009;Sato et al., 2014b). In extreme cases, this lack of contemporary connectivity can erode genetic diversity sufficiently within fragments to reduce population-level fitness, which elevates extinction risk (Maron et al., 2015). ...
... In this context, genome-wide measures of intra-population genetic diversity are important as they allow us to determine population viability and susceptibility to disturbance (Demos et al., 2015), as well as to identify and protect important habitat corridors to ensure ongoing gene flow (Coulon et al., 2004). Attaining genetic insight at higher resolutions can identify processes that have shaped the structure of allopatric populations and allow for more informed conservation management of alpine endemic species (Koumoundouros et al., 2009;Haines et al., 2017). Such knowledge is increasingly important as climate warming reduces the extent of the alpine zone, further isolating populations and enhancing the likelihood of species extinctions (Dirnb€ ock et al., 2011). ...
... A previous phylogeographic study using a single mitochondrial gene and extremely limited sampling across the species range, suggests that L. guthega may be highly structured throughout its range . The topographic variability of the Great Diving Range that separates L. guthega populations has also been shown to influence the population structure of other Australian sky-island taxa (Mitrovski et al., 2007;Koumoundouros et al., 2009;Tatarnic et al., 2013;Slatyer et al., 2014). Due to limited connectivity among Australian sky-island regions, coupled with the reduced extent of the Australian alpine zone, we predicted that L. guthega show high genetic divergence between geographically separated populations and exhibit low levels of genetic diversity within populations. ...
... Population genetics research has provided information critical for conservation management and, in the case of the alpine she-oak skink Cyclodomorphus praealtus, has contributed to a successful submission for federal endangered species status. Despite this progress, relatively few studies have focused on sky island species from the Australian Alps (but see Osborne et al. 2000;Mitrovski et al. 2007;Morgan et al. 2008;Koumoundouros et al. 2009;Tatarnic et al. 2013;Slatyer et al. 2014;Endo et al. 2015). ...
... However, the high genetic diversity at BL/ST may also be due to this region comprising two areas of high elevation that likely formed a larger, continuous habitat during glacial periods compared to the other study sites. The correlation between higher elevation and greater genetic diversity has been observed in alpine she-oak skinks (Koumoundouros et al. 2009), but was not supported for mountain pygmy possums (Mitrovski et al. 2007). ...
... Overall, the genetic structuring in the mtDNA and microsatellite datasets is consistent with those observed in sympatric, alpine restricted taxa. Mitochondrial introgression was detected between P. cryodroma populations at neighboring BHP and HT in concordance with genetic studies on the mountain pygmy possum (Osborne et al. 2000;Mitrovski et al. 2007), alpine she-oak skink (Koumoundouros et al. 2009), and several invertebrate species (Tatarnic et al. 2013;Slatyer et al. 2014;Endo et al. 2015). These observations withstanding, based on microsatellite data, contemporary introgression was not detected between populations of P. cryodroma, mountain pygmy possums, alpine she-oak skinks, or alpine grasshoppers, Kosciuscola tristis, from BHP and HT. ...
Article
Full-text available
Species endemic to sky island systems are isolated to mountain peaks and high elevation plateaux both geographically and ecologically, making them particularly vulnerable to the effects of climate change. Pressures associated with climate change have already been linked to local extinctions of montane species, emphasizing the importance of understanding the genetic diversity and population connectivity within sky islands systems for the conservation management of remaining populations. Our study focuses on the endangered alpine skink Pseudemoia cryodroma, which is endemic to the Victorian Alps in south-eastern Australia, and has a disjunct distribution in montane habitats above 1100 m a.s.l. Using mitochondrial DNA (mtDNA) and microsatellite loci, we investigated species delimitation, genetic connectivity and population genetic structure across the geographic range of this species. We found discordance between genetic markers, indicating historical mtDNA introgression at one of the study sites between P. cryodroma and the closely related, syntopic P. entrecasteauxii. Molecular diversity was positively associated with site elevation and extent of suitable habitat, with inbreeding detected in three of the five populations. These results demonstrate the complex interaction between geography and habitat in shaping the population structure and genetic diversity of P. cryodroma, and highlight the importance of minimising future habitat loss and fragmentation for the long-term persistence of this species.
... Phylogeographic studies of Australian alpine biota are limited to a small number of mammals (Osborne et al., 2000;Mitrovski et al., 2007), reptiles (Chapple et al., 2005;Koumoundouros et al., 2009) and invertebrate species (Tatarnic et al., 2013) and have focused mostly on different geographic regions. Nevertheless, patterns emerging from these studies point to greater divergence among regions than might be expected based on the connectedness of mountain habitats. ...
... Nevertheless, patterns emerging from these studies point to greater divergence among regions than might be expected based on the connectedness of mountain habitats. Phylogeographic analysis of the Australian alpine lizard Cyclodomomorphus praealtus indicates deep genetic differentiation between sky-island populations over short geographic distances (< 40 km in some cases), indicating historical isolation and Pleistocene diversification (Koumoundouros et al., 2009). Similar patterns have also been observed in the alpine skinks Egernia guthega and E. montana (Chapple et al., 2005). ...
... The high level of intraspecific divergence in the Victorian Alpine region does not seem to be related to vagility, given that it has been observed in a variety of organisms (Osborne et al., 2000;Chapple et al., 2005;Mitrovski et al., 2007;Schmitt, 2007;Koumoundouros et al., 2009;Schoville & Roderick, 2009). As discussed previously, the snowline was approximately 800 m lower than in the present day during the most recent glacial advances, and connected much of the alpine habitat across the region (Galloway, 1965;Fig. ...
Article
Full-text available
Comparative phylogeographic analyses of alpine biota from the Northern Hemisphere have linked patterns of genetic diversification to glacial expansion and contraction events in the Pliocene and Pleistocene. Furthermore, the extent of diversification across species groups appears to be associated with vagility. In this study we test whether these patterns apply to a geologically stable system from eastern Australia with comparatively shallow elevational gradients and minimal influence from historical glacial activity.
... mountain katydid Acripeza reticulata, bogong moth Agritos infusa, the spotted mountain grasshopper Monistria concinna, metallic cockroach Polyzosteria viridissima (Green and Osborne 1994) and glow worm Arachnocampa buffaloensis (Baker et al. 2008)). Our results show similar broad scale patterns to phylogenies of other alpine groups such as lizards (Chapple et al. 2005;Koumoundouros et al. 2009), endangered frogs (Morgan et al. 2008) and endangered marsupials (Osborne et al. 2000;Mitrovski et al. 2007). These groups show splits between NSW and Victorian populations, which are generally attributed to the extensive passage of lowlands and the Murray River that runs westeast between the plateaus (Koumoundouros et al. 2009). ...
... Our results show similar broad scale patterns to phylogenies of other alpine groups such as lizards (Chapple et al. 2005;Koumoundouros et al. 2009), endangered frogs (Morgan et al. 2008) and endangered marsupials (Osborne et al. 2000;Mitrovski et al. 2007). These groups show splits between NSW and Victorian populations, which are generally attributed to the extensive passage of lowlands and the Murray River that runs westeast between the plateaus (Koumoundouros et al. 2009). In K. tristis, the presence of an analogous split is equivocal. ...
... The percentage sequence divergence (percentage of sites in the alignment where bases differ) between northern and southern K. tristis is intermediate compared with those reported for other groups. For example the percentage sequence divergence between grasshoppers from the Road to Dargo, Mt Hotham, Vic. and Dead Horse Gap, NSW is 3.3%, compared with 4.3% for the alpine she-oak skink (Koumoundouros et al. 2009) or 1.1% for the mountain pygmy possum (Mitrovski et al. 2007). Assuming mutation rates for Australian Orthoptera are similar to those recorded in North America (Knowles 2000), we tentatively suggest that a percentage divergence of 3.3% between the northern and southern populations of K. tristis equates to a divergence time of around 1.4 million years ago. ...
Article
Full-text available
Diversity and speciation in Australia's alpine biota are poorly understood. Here we present a molecular phylogeny of the Australian alpine grasshopper genus Kosciuscola (Sjösted) that currently includes five described species. These grasshoppers are of interest not only because of their alpine distribution but also for the extraordinary colour change exhibited by the species K. tristis, whose males turn turquoise when their body temperature exceeds 25 C. We reconstructed the phylogeny with two fragments of the mitochondrial genome using parsimony, maximum likelihood and Bayesian analyses and our data support the current taxonomy. Further, our data show little geographic structuring within some clades, which is puzzling since members of Kosciuscola are brachypterous. Finally, our data coupled with our observations on colouration provide evidence for a genetically distinct clade of K. tristis in the Victorian Alps. This is among the first molecular studies of an alpine invertebrate and one of a few on non-endangered, widespread Australian alpine species. More phylogenetic studies in the Australian Alps are required if we are to understand the evolution of alpine fauna and establish baseline data to monitor their response to climate change.
... mountain katydid Acripeza reticulata, bogong moth Agritos infusa, the spotted mountain grasshopper Monistria concinna, metallic cockroach Polyzosteria viridissima (Green and Osborne 1994) and glow worm Arachnocampa buffaloensis (Baker et al. 2008)). Our results show similar broad scale patterns to phylogenies of other alpine groups such as lizards (Chapple et al. 2005;Koumoundouros et al. 2009), endangered frogs (Morgan et al. 2008) and endangered marsupials (Osborne et al. 2000;Mitrovski et al. 2007). These groups show splits between NSW and Victorian populations, which are generally attributed to the extensive passage of lowlands and the Murray River that runs westeast between the plateaus (Koumoundouros et al. 2009). ...
... Our results show similar broad scale patterns to phylogenies of other alpine groups such as lizards (Chapple et al. 2005;Koumoundouros et al. 2009), endangered frogs (Morgan et al. 2008) and endangered marsupials (Osborne et al. 2000;Mitrovski et al. 2007). These groups show splits between NSW and Victorian populations, which are generally attributed to the extensive passage of lowlands and the Murray River that runs westeast between the plateaus (Koumoundouros et al. 2009). In K. tristis, the presence of an analogous split is equivocal. ...
... The percentage sequence divergence (percentage of sites in the alignment where bases differ) between northern and southern K. tristis is intermediate compared with those reported for other groups. For example the percentage sequence divergence between grasshoppers from the Road to Dargo, Mt Hotham, Vic. and Dead Horse Gap, NSW is 3.3%, compared with 4.3% for the alpine she-oak skink (Koumoundouros et al. 2009) or 1.1% for the mountain pygmy possum (Mitrovski et al. 2007). Assuming mutation rates for Australian Orthoptera are similar to those recorded in North America (Knowles 2000), we tentatively suggest that a percentage divergence of 3.3% between the northern and southern populations of K. tristis equates to a divergence time of around 1.4 million years ago. ...
Data
Full-text available
Diversity and speciation in Australia's alpine biota are poorly understood. Here we present a molecular phylogeny of the Australian alpine grasshopper genus Kosciuscola (Sjösted) that currently includes five described species. These grasshoppers are of interest not only because of their alpine distribution but also for the extraordinary colour change exhibited by the species K. tristis, whose males turn turquoise when their body temperature exceeds 25 C. We reconstructed the phylogeny with two fragments of the mitochondrial genome using parsimony, maximum likelihood and Bayesian analyses and our data support the current taxonomy. Further, our data show little geographic structuring within some clades, which is puzzling since members of Kosciuscola are brachypterous. Finally, our data coupled with our observations on colouration provide evidence for a genetically distinct clade of K. tristis in the Victorian Alps. This is among the first molecular studies of an alpine invertebrate and one of a few on non-endangered, widespread Australian alpine species. More phylogenetic studies in the Australian Alps are required if we are to understand the evolution of alpine fauna and establish baseline data to monitor their response to climate change.
... Notably, Australia's sky island species face an uncertain future (Parida et al. 2015;Sritharan et al. 2021) due to warming temperatures and relatively low mountain elevations (McGowan et al. 2018). Genetic studies in Australia's mainland Alps have identified signals of isolation by distance or landscape barriers in reptiles (Chapple et al. 2005;Koumoundouros et al. 2009;Haines et al. 2017;Atkins et al. 2019), amphibians (Banks et al. 2020), mammals (Mitrovski et al. 2007) and invertebrates (Endo et al. 2015). These studies commonly identified genetic differentiation between populations on Kosciuszko Plateau and the smaller southern plateaus, and linked past fluxes in connectivity and isolation to glacial periods, consistent with evidence of climate-driven fragmentation on other continents (Chala et al. 2017;Mastretta-Yanes et al. 2018;Wiens et al. 2019;Tonzo & Ortego 2021). ...
... These studies commonly identified genetic differentiation between populations on Kosciuszko Plateau and the smaller southern plateaus, and linked past fluxes in connectivity and isolation to glacial periods, consistent with evidence of climate-driven fragmentation on other continents (Chala et al. 2017;Mastretta-Yanes et al. 2018;Wiens et al. 2019;Tonzo & Ortego 2021). One such study identified alpine she-oak skink (Cyclodomorphus praealtus Shea 1995; Scincidae) populations from Kosciuszko Plateau and the southern plateaus as two Evolutionary Significant Units (Koumoundouros et al. 2009). However, that study had low sample numbers from Kosciuszko Plateau (n = 5, from a single location) and additional occupied sites have since been identified, extending the species' known range (Clemann et al. 2016;NSW Environment Energy and Science 2021). ...
Article
Full-text available
Sky island species face climate-driven and anthropogenic habitat loss and population fragmentation, and are therefore vulnerable to genetic erosion. We conducted a genetic study of the cryptic and threatened alpine she-oak skink (Cyclodomorphus praealtus) throughout its range, across two regions of the mainland Australian Alps; an extensive high elevation plateau in the north (‘Kosciuszko Plateau’) and several smaller plateaus in the south (‘southern plateaus’). We investigated whether extensive potential habitat across Kosciuszko Plateau supported larger, connected populations with better genetic health than more fragmented southern plateaus. Our analyses of genome-wide markers confirmed effective isolation of the two regions. We identified three populations from the southern plateaus, largely aligning with discrete landforms, and four populations on Kosciuszko Plateau. Only one individual, from the southern-most population, showed evidence of admixture between the two regions. Across its range, C. praealtus populations had low genetic diversity and small effective population sizes. In contrast to our expectations, Kosciuszko Plateau populations were smaller, with greater genetic differentiation and a higher degree of inbreeding than the southern populations. We detected admixture between populations on Kosciuszko Plateau, while the southern plateaus had limited admixture. We found no evidence of local adaptation, suggesting plateaus represent interglacial refugia. Our results suggest that C. praealtus has little capacity to withstand further disturbance or rapid environmental changes. Maintaining or restoring habitat quality in occupied and suitable connecting habitats across the species’ range is paramount. ‘Genetic rescue’ should be investigated as an option to mitigate the effects of isolation and improve population resilience.
... Adaptations to different climatic conditions are a key determinate of an ectotherm's geographic range (Monasterio et al. 2016). Present day alpine endemics are generally restricted to 'sky islands' of suitable alpine habitat and may have physiological adaptations to cold climates (Koumoundouros et al. 2009). Differences in climatic tolerance between species, and poor dispersal, can shape community structure in this group. ...
... praealtus) and Guthega skink (Liopholis guthega; Sato et al. 2014a). These species are alpine endemics, confined to two main regions within the Australian mainland alps (Koumoundouros et al. 2009;Atkins et al. 2020). The isolation of the highelevation environment in Australia has facilitated high rates of endemism within this region, and several species are listed as Threatened (e.g. C. praealtus, Clemann et al. 2018a;L. ...
Article
The rapid changes in altitude, and associated habitat, of mountain ecosystems make them ideal natural laboratories for testing the effect of environmental heterogeneity on species assemblage. Our understanding of the sensitivity of Australian reptiles to elevational clines is limited. We examined lizard distribution across three elevation zones (montane, subalpine and alpine), spanning from 900 to 1840 m above sea level, in the Australian alps. We aimed to examine how elevation influences species diversity and abundance, and ectoparasite load, and whether species alter their habitat use amongst different elevational zones. Active searches were conducted across the elevation zones to identify lizard community structure (at least 16 species) across elevational zones, along with skink habitat preferences and the ectoparasite load. Skink diversity and abundance were negatively correlated with increased elevation. The alpine zone had significantly lower diversity and abundance of skinks. Habitat use differed amongst both elevations and species. Ectoparasite prevalence was also significantly diminished in the alpine zone. Ectoparasites only infected a subset of the skink community, with ectoparasite load increasing as the active season progressed. This study provides evidence of the complex interplay between elevation and species diversity, as well as the differences in ectoparasite pressure along elevational gradients in the Australian alps.
... Understanding patterns of gene flow is crucial for the design of effective conservation strategies for threatened reptiles (Koumoundouros et al., 2013). Phenotypic divergence is aligned with genomic divergence in response to changes in climate (Prates et al., 2016), due to the connection between long-term evolutionary adaptation to an environmental selective agent and short-term stress response in individual organisms . ...
... Species that are restricted to habitat fragments, especially if population subdivisions persisted over evolutionary time and have generated genetic discontinuity across the species' range, should present higher vulnerability to climate change if the sites that contain most of the species' genetic variation would be also among the most affected areas (Clark et al., 2011;Dubey et al., 2013;Koumoundouros et al., 2013). When connectivity between suitable patches is reduced and estimates are of low gene flow between populations, the implication is that distance between fragments will increase, which can lead to two consequences: vicariance through fragmentation, which demands an increase in population size and ecological requirements, or a possible local extinction if these factors decreases rather than increases, which in a scenario of climate change is more likely to occur ). ...
Article
In recent decades, changes in climate have caused impacts on natural and human systems on all continents and across the oceans and many species have shifted their geographic ranges, seasonal activities, migration patterns, abundances and interactions in response to these changes. Projections of future climate change are uncertain, but the Earth’s warming is likely to exceed 4.8°C by the end of 21th century. The vulnerability of a population, species, group or system due to climate change is a function of impact of the changes on the evaluated system (exposure and sensitivity) and adaptive capacity as a response to this impact, and the relationship between these elements will determine the degree of species vulnerability. Predicting the potential future risks to biodiversity caused by climate change has become an extremely active field of research, and several studies in the last two decades had focused on determining possible impacts of climate change on Lepidosaurians, at a global, regional and local level. Here we conducted a systematic review of published studies in order to seek to what extent the accumulated knowledge currently allow us to identify potential trends or patterns regarding climate change effects on lizards, snakes, amphisbaenians and tuatara. We conducted a literature search among online literature databases/catalogues and recorded 255 studies addressing the influence of climate change on a total of 1918 species among 49 Lepidosaurian’s families. The first study addressing this subject is dated 1999. Most of the studies focused on species distribution, followed by thermal constraints, reproductive biology, behavior and genetics. We concluded that an integrative approach including most of these characteristics and also bioclimatic and environmental variables, may lead to consistent and truly effective strategies for species conservation, aiming to buffer the climate change effects on this group of reptiles.
... For example, the alpine bioregion of south-eastern Australia has several reptile taxa that are restricted to disjunct, high-elevation peaks and plains in this region (e.g. alpine she-oak skink and guthega skink, Liopholis guthega: Koumoundouros et al. 2009). ...
... In a review of the FFG Act, the Victorian Auditor-General (2009) criticised the level of resourcing for threatened species planning in the State. Collaborative efforts between multiple people and agencies can bring synergies to research and management of threatened species that maximise the benefits attained from resource investment; recent examples that have benefited threatened reptiles in Victoria include works by Koumoundouros et al. (2009) andMaldonado et al. (2012). ...
Article
For the first time in the history of life, a biodiversity extinction crisis is being driven by a single species - humans. Humans also have unprecedented control over both the threats and conservation actions that influence this crisis. When prioritising conservation actions, innate human bias often favours endothermic vertebrates over other fauna. Reptiles are the least popular terrestrial vertebrate class, and consequently are particularly disadvantaged in terms of being listed as threatened and receiving conservation management. Despite 30 years of formally evaluating and listing threatened vertebrates in the Australian State of Victoria, there is a strong worsening trend in the conservation status of all faunal groups. The deteriorating status of Victorian reptiles mirrors worrying documented trends in reptile conservation status around the world. I review the history of listing threatened reptiles in Victoria, detail worsening trends in their conservation status, and suggest that, as in other parts of the world, the threats common to most listed taxa are climate change, habitat loss and degradation, and elevated rates of predation by exotic predators. I also identify poor advice and planning as a considerable threat to Victorian reptiles; this threat is rarely reported, but may be more pervasive than currently recognised. I argue that what is needed for most reptiles to have the greatest chance of persisting in the long term is prevention of habitat loss and degradation, research to underpin listing and management, improved policy so that unproven management strategies are not sanctioned, and vetting of consultant's reports so that unproven 'mitigation' strategies and inadequate preimpact surveys do not mask the true cost of loss and degradation of habitat
... The most extensive areas of alpine and sub-alpine habitat in Australia, lying within the Kosciuszko region in New South Wales and the Bogong High Plains in Victoria, are separated by approximately 100 km of lowland across the Murray River valley, which also marks the State border ( Figure 1a). This geographic discontinuity represents a significant divergence point for several alpine reptile and mammalian species [21][22][23]. For example, the skink Egernia guthega, an alpine endemic, shows an average 2.2% mitochondrial (ND4) sequence divergence between a population from Kosciuszko and three populations from the Bogong High Plains. ...
... Depression of the snowline during glacial periods is thought to have resulted in continuous alpine/sub-alpine conditions from Mt Jagungal into southern Victoria [15,16]. While this depression might have facilitated range expansion and, consequently, low differentiation across the alpine area as a whole [9,48], previous studies on geographic subsets of Australia's high country have found high endemism among mountain suggesting relatively stable population histories and isolation among mountains [17,21,22]. In particular, considering both the sequence and microsatellite datasets, we identify four primary genetic groups: two southern Victorian groups comprising Mt Baw Baw and Mt Buller/Mt Stirling; a Bogong High Plains cluster comprising the Bogong High Plains proper and Mt Buffalo; and a Kosciuszko cluster. ...
Article
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Background Mountain landscapes are topographically complex, creating discontinuous `islands¿ of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia¿s high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia¿s mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted).ResultsWe found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance.Conclusions Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia¿s alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation, divergence among populations was on the same scale as that detected in much more extensive Northern hemisphere mountain systems. The processes driving divergence in the Australian mountains might therefore differ from their Northern hemisphere counterparts.
... Spatial genetic patterns are increasingly studied and applied to management decisions for threatened species, including identification of conservation units and estimation of dispersal and migration (Schwartz et al. 2007;Elderkin et al. 2008;Koumoundouros et al. 2009). Understanding the origins of contemporary genetic population structure can also contribute valuable information in the guidance of management programs (Leonard 2008;Shepherd and Lambert 2008;Boessenkool et al. 2009). ...
... Humans have significantly changed the landscape through burning and clear-felling large tracts of forest and introducing exotic mammalian predators. Introduced predators, such as stoats (Mustela erminea), ship rats (Rattus rattus) and brushtail possums (Trichosurus vulpecula) pose a severe threat to many native bird species, including mohua (King 1984). Mohua are currently listed as 'endangered' by the IUCN Red List of Threatened Species (IUCN 2010) and as 'nationally endangered' by the New Zealand Threat Classification System List (Hitchmough et al. 2007). ...
Article
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Contemporary patterns of genetic structure among fragmented populations can either result from historic patterns or arise from human-induced fragmentation. Use of historic samples collected prior to fragmentation allows for the origin of genetic structure to be established and appropriate management steps to be determined. In this study, we compare historic and contemporary levels of genetic diversity and structure of an endangered passerine, the New Zealand mohua or yellowhead (Mohoua ochrocephala), using nuclear microsatellites. We found that a significant amount of allelic richness has been lost over the last 100 years. Close to half of this was due to extinction of birds from entire regions, but almost as much was due to loss of genetic diversity within extant populations. We found a pattern of isolation by distance among contemporary populations, which could have resulted from historic structure due to limited gene flow along a latitudinal cline. However, we found that minimal genetic structure existed historically. The pattern of increased structure over time was confirmed by factorial correspondence analysis. We conclude that the genetic structure apparent today resulted from anthropogenic effects of recent fragmentation and isolation. We emphasize the importance of assessing genetic structure of populations prior to their fragmentation, when determining the significance of contemporary patterns. This study highlights the growing importance of museum specimens as a tool in the conservation of threatened and endangered species. KeywordsGenetic structure–Historic DNA– Mohoua ochrocephala –Microsatellites–Genetic diversity–Wildlife conservation
... The presence or formation of geographic barriers such as mountains, rivers or oceans may act to physically separate populations within a species (Lomolino et al. 2006;Whittaker and Fernandez-Palacios 2007). The occurrence of such barriers limits or prevents dispersal, and often leads to reduced gene flow and connectivity among populations (Slatkin 1987;Koumoundouros et al. 2009). Genetic drift and local adaptation may lead to the genetic and phenotypic divergence of each isolated population, and over time might result in the populations no longer being capable of interbreeding (Dobzhansky 1940;Hoskin et al. 2005). ...
Article
Human-mediated dispersal of animals often acts to bring populations that have been separated for substantial periods of evolutionary time (e.g. millions of years) in their native range into contact in their introduced range. Whether these taxa successfully interbreed in the introduced range provides information on the strength of reproductive isolation amongst them. The invasive delicate skink (Lampropholis delicata) has been accidentally introduced to Lord Howe Island from four genetically divergent (>2 million years) regions of the species’ native range in eastern Australia. We used mitochondrial DNA and microsatellite data to investigate whether the individuals from four of the native-range source regions are interbreeding on Lord Howe Island. Our analyses indicate that intraspecific hybridisation among individuals from all four native-range source regions is occurring. Although there is little evidence for hybrids in the northern end of Lord Howe Island (proportion of hybrids: 0–0.02; n = 31), there is a high proportion of hybrids in the central (0.33–0.69; n = 59) and southern regions (0.38–0.75; n = 8) of the island. Given the strong evidence for interbreeding among all four native-range source regions examined, and the relatively minor morphological, life-history and phenotypic variation among them, we suggest that the delicate skink should continue to be treated as a single, widespread, but variable species.
... The same data also provide essential information to conservation managers. Species that appear widespread may in fact be represented by a series of isolated sub-populations with varying demographic and diversity characteristics, and their genetic and phenotypic diversity may therefore be at higher risk of extinction than they first appear (Frankham et al., 2002;Koumoundouros et al., 2009). Small isolated populations with low genetic diversity are at greater risk of the effects of inbreeding, genetic drift, and potentially extinction, each of which are critical contributors to specieslevel evolutionary and management processes (Bakker et al., 2010;Frankham, 2005;Frankham et al., 1999Frankham et al., , 2002. ...
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This research investigates the extent and causal mechanisms of genetic population divergence in a poorly flighted passerine, the North Island Rifleman or Titipounamu (Acanthisitta chloris granti). While this species has a historically widespread distribution, anthropogenic forest clearance has resulted in a highly fragmented current distribution. We conducted analyses of mitochondrial DNA (COI and Control Region) and 12 nuclear DNA microsatellites to test for population divergence and estimate times of divergence. DiyAbc and BioGeoBears were then used to assess likely past dispersal scenarios based on both mtDNA and nDNA. The results reveal several significantly divergent lineages across the North Island of New Zealand and indicate that some populations have been isolated for extensive periods of time (0.7–4.9 mya). Modeling indicated a dynamic history of population connectivity, with a drastic restriction in gene flow between three geographic regions, followed by a more recent re‐establishment of connectivity. Our analyses indicate the dynamic influence of key geological and climatological events on the distribution of genetic diversity in this species, including support for the genetic impact of old biogeographic boundaries such as the Taupo Line and Cockayne's Line, rather than recent anthropogenic habitat fragmentation. These findings present a rare example of an avian species with a genetic history more like that of flightless taxa and so provide new general insights into vicariant processes affecting populations of passerines with limited dispersal.
... lack of shared haplotypes among populations other than for the MN-WS. This population structure was likely a consequence of low dispersal ability of lizards (Clark et al., 1999;Dubey & Shine, 2010;Koumoundouros et al., 2009;Orsini et al., 2013). Dispersal of Leiolepis seems to be limited by their behaviors and life history (Arunyavalai, 2003). ...
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Leiolepis ocellata is a lizard species distributing in topographically diverse habitats in northern Thailand. To explore its evolutionary history, 113 samples of L. ocellata were collected from 11 localities covering its distributional range in northern Thailand, and sequenced for mtDNA fragments (Cyt b and ND2). Pairwise comparisons across sampling localities yielded significant genetic differentiation (FST and Jost's D) but no clear pattern of isolation by distance could be demonstrated based on the Mantel test. Phylogenetic and network analyses highlighted six haplogroups. Their divergence times were estimated to occur during the Pleistocene, much more recent than major orogenic events affecting northern Thailand. Instead, the results suggested that lineage divergences, of particularly eastern and western haplogroups of the region, coincided with the major rivers in the region (Yom river and Ping river, respectively), indicating vicariance in response to riverine barriers. Furthermore, ecological niche modeling suggested an expansion of suitable habitats of L. ocellata, when LGM‐liked conditions. This expansion potentially facilitated their dispersal among adjacent localities leading to lineage diversification and genetic admixture, after the riverine divergence.
... Consequently, their introduction and burgeoning population size have strong negative impacts on both native species and ecosystems that have not adapted to horse disturbance. For example, the alpine she-oak skink (Cyclodomorphus praealtus), an endangered species that inhabits treeless sub-alpine grasslands (Koumoundouros et al., 2009), is heavily dependent on tall tussock grasses for basking (Clemann, 2003). Other rodents such as the bush rat also use grass tussocks for shelter and movement. ...
Article
Feral (wild) horses present significant challenges for landscape managers. A major effect of horses is trampling, which erodes soil and alters vegetation cover, which is often critical habitat for threatened animals. We examined the direct and indirect impacts of horses, kangaroos, and rabbits on the broad-toothed rat (Mastacomys fuscus), a threatened rodent in subalpine grasslands in Kosciusko National Park, which contains a large wild horse population. Our objective was to examine the relationship between the activity of different herbivores and 1) structural attributes of the vegetation (cover and density of different plant groups) and 2) length of broad-toothed rat runways and the presence of scat along these runways as proxies of broad-toothed rat activity. We assessed herbivore activity and measured vegetation cover, structure, and richness and total length of runways used by broad-toothed rats as a measure of activity. We used structural equation modeling to test the hypothesis that horse activity would lead to reductions in rat habitat directly, by increasing disturbance, and indirectly, by altering vegetation structure. Quadrats showing no evidence of horse activity had longer broad-toothed rat runways, taller but fewer grasses, double the shrub cover, and lower plant richness than quadrats showing evidence of horse activity. Structural equation modeling showed that there were no significant direct associations between horse activity and rat activity. However, increasing horse activity was associated with an indirect negative effect on broad-toothed rat activity by suppressing the positive relationship between grass height and rat activity. There were no significant effects of rabbits on any environmental variables, and kangaroo grazing was associated with an increase in shrub cover only. Disturbance by horses likely alters vegetation structure, by reducing grass height, making it less suitable for broad-toothed rats, thereby reducing their populations. Horses should be restricted from accessing critical broad-toothed rat habitat.
... I used a Wilcoxon signed-rank test as suggested by Cornuet and Luikart (1996) and the two-phase mutation model (TPS; Di Rienzo et al. 1994) with a range of parameter settings for the proportion of multi-step mutations and the mean size of multi-step mutations. The range of parameter settings included those previously used with lizards (Koumoundouros et al. 2009), and with birds (Miller et al. 2012). The relative roles of drift and gene flow on population structure were investigated following Jordan and Snell (2008). ...
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How and under what situations populations adapt to local conditions remains a key question in evolutionary biology. This study tests if the particular morphology of a population of Tree lizards, Urosaurus ornatus, located in a canyon on the margin of the species range represents an adaptation to canyon habitat. Morphology was compared across 40 populations showing that relative hind limb length, tail length, and mass were all outliers for this population. The function of the relatively longer hind limbs, tail, and lower mass was proposed to be for better sprinting ability on the sheer canyon walls that provide the only available habitat structure for this population. Partial least squares regression found significant effects of tail length on top speed on a broad, steep surface. Partial least squares logistic regression identified significant effects of tail length on survival as well in males but not females of this population. Another canyon population of Tree lizards with access to alternative substrates (trees) showed no evidence of selection on the same morphological features. Ancestral state reconstruction using a phylogeny inferred for 21 populations found that the unique morphology of the focal population was evolutionarily derived compared to closely related populations and so likely arose under the present environmental conditions. Population genetic structure also supported the process of adaptive divergence as there was no evidence for migration and/or a recent genetic bottleneck in the focal population. Lizards in this population appear to have responded to selection allowing them to become specialists for running on canyon walls while other canyon populations with access to a greater variety of habitat structure have not.
... Genetic analyses of Australian alpine fauna indicate high levels of genetic structuring at fine spatial scales, with evidence of deep lineage splits among summit communities, including those connected by high-elevation plateaus (Chapple, Keogh, & Hutchinson, 2005;Endo et al., 2015;Hatley & Murphy, 2016;Koumoundouros, Sumner, Clemann, & Stuart-Fox, 2009;Mitrovski, Heinze, Broome, Hoffmann, & Weeks, 2007;Osborne, Norman, Christidis, & Murray, 2000). These patterns differ markedly from Northern Hemisphere alpine systems, where shallow genetic differentiation is typically observed among populations owing to a history of post-glacial expansion (e.g., Buckley, Simon, Shimodaira, & Chambers, 2001;Ikeda, Senni, Fujii, & Setoguchi, 2008;Kubow, Robinson, Shama, & Jokela, 2010;Todisco et al., 2012). ...
... To establish resilient landscapes, large, intense, and continuous fires are known to produce environmental homogeny (Williams et al., 2009;Keith, 2012), conditions that have the potential to drive species toward extinction . Fire can degrade habitat and fragment populations of wildlife; deleteriously affecting population size, migration rates, and genetic diversity, and can ultimately lead to biodiversity loss and local extinctions (Fenner and Bull, 2007;Koumoundouros et al., 2009;Dubey and Shine, 2010). The direct effect of fire on wildlife can only be ascertained through reliable pre-and postfire species information (Clarke, 2008). ...
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Species' tolerance of and response to fire varies. Environments that experience frequent fires will contain fire-tolerant fauna, whereas fauna that occur in environments that burn infrequently may lack strategies to cope with fire. In 2003, intense summer wildfires in southeastern Australia's alpine region burned more than 1.3 million ha. The Guthega Skink, Liopholis guthega, is an endangered lizard that is restricted to two geographically isolated alpine locations affected by these fires: Kosciuszko National Park in New South Wales, and the Bogong High Plains in Victoria. We investigated the long-term effects of fire on L. guthega populations through surveys of burned and unburned habitat on the Bogong High Plains. We found L. guthega selected specific microhabitats that are restricted on the Bogong High Plains. Their selection of less-vegetated microhabitats suggests that they may favor an early successional environment. We found retreat site selection differed between sites; at burned sites L. guthega burrowed preferentially under rocks, and at unburned sites comparatively more burrows were positioned at the base of shrubs. Our results suggest that in this species' Victorian range they may be more tolerant to fire than previously thought, likely because of the protection afforded by their burrows. However, our surveys of L. guthega populations from past records also suggest potential local extinctions. To determine the immediate and longer-term effects of intense fires on threatened species, it is important to have prefire data on species and prompt postfire assessments to obtain results applicable to management.
... Cyclina sinensis (authors' unpubl. data); (e) clam Tegillarca granosa (present study) Campbell et al. 2009, Koumoundouros et al. 2009). The 2 T. granosa ESUs we identify here can aid sustainable management of this clam by helping to define conservation priorities (e.g. ...
Article
Present genetic patterns of marine organisms not only result from historical and contemporary ecological factors, but also from anthropogenic activities. Disentangling the relative effects of these factors can provide valuable insights into management and protection of exploitable species. The commercially important marine clam Tegillarca granosa is representative of species that are translocated within East Asia for coastal aquaculture purposes. We conducted a nucleotide sequence analysis of mitochondrial cytochrome c oxidase subunit I and nuclear internal transcribed spacer 1 markers in T. granosa to investigate its genetic diversity and distribution in 2 marginal seas (the East and South China Seas) of the northwestern Pacific. Based on phylogenetic inferences, we identified 2 evolutionarily significant units (ESUs) with high genetic distance between them for both markers. The high genetic distance may be associated with the historical isolation of the marginal seas during low sea level periods. One ESU was widely distributed in both seas, whereas the other was restricted to 2 disjunct localities in the South China Sea. Based on the isolation by distance analysis (p = 0.068) and comparison of patterns of co-occurring species, this pattern appears to be mostly attributable to the human-mediated translocations among coastal waters rather than natural range expansion. Furthermore, from a conservation viewpoint, the southern ESU is now facing high extinction risk because of mitochondrial introgression and smaller, fragmented populations; consequently, immediate proper management is required to protect the endangered populations representing this lineage.
... this pathogen is correct (see McCallum 2005 for discussion of this hypothesis), it is possible that some isolated frog populations have remained pathogen free. This suggestion is most likely on offshore islands and in high altitude areas isolated by steep / dissected country (i.e., "sky islands" sensuKoumoundouros et al. 2009), that would restrict the movement of vectors for the Amphibian Chytrid Fungus. Our results suggest that the Grey Mare Range site may be free of Amphibian Chytrid Fungus possibly because this site is relatively isolated from other areas of frog habitat by considerable distance and terrain that is unlikely to be crossed by frogs. ...
... entrecasteauxii A), presumably due to differences in ecology. In alpine and sub-alpine areas Pseudemoia pagenstecheri is typically restricted to grasslands on disjunct plateaux (Wilson and Swan, 2013), which may have caused it to experience greater habitat fragmentation and therefore greater barriers to gene flow (Koumoundouros et al., 2009). In contrast, P. entrecasteauxii is a more generalist species occurring in a wider range of habitats (Wilson and Swan, 2013), allowing gene flow to be more continuous between occupied areas. ...
... Migration potential is limited in the alps, but studies in plants indicate both plastic and adaptive responses to environmental gradients (e.g. ). The adaptive potential of alpine animals has not been thoroughly studied, but low dispersal and gene flow between populations (Koumoundouros et al. 2009;Mitrovski et al. 2007) is likely to limit rapid adaptation. Thus, phenoytpic plasticity is likely to be an important determinant of a species' resistance to climate change and this is a key area for future research. ...
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Global ambient temperatures have increased significantly (average 0.7°C) over the last century. In high-altitude areas, concurrent changes in precipitation regimes are already having a noticeable impact on snow area, depth and persistence in alpine and subalpine zones. Australia's alpine habitat is limited, covering only approximately 0.15% of the continent. Changes in snow regimes predicted under future climate change are likely to have a significant impact on the animals and plants whose ecology is intrinsically linked to snow conditions. For small mammals, reduced snow depth and area will reduce the availability of suitable over-wintering habitat and could increase predation. However, these effects are species-specific. Changes in snow regimes are predicted to significantly alter the composition and distribution of alpine vegetation communities. In particular, movement of species ranges to higher altitudes is predicted to increase species diversity in the alpine zone (though with a likely loss of some species). Wildfires poses an additional threat to alpine plants and animals, with many species apparently vulnerable to an increase in fire frequency. However, they appear to be resilient to high wildfire intensity. Thus, while climate change presents a significant threat to Australia's alpine ecosystems, the specific impacts will depend on the resilience and adaptability of individual species.
... However, in our study, the highelevation regions of the Bogong High Plains, nearby Mt Hotham, and more northerly Mt Kosciuszko, were not distinguished from each other, nor from the westerly lower elevation Lake Mountain sample. For alpine-restricted species in Australia and elsewhere, the alpine zone has been considered a chain of 'sky islands'with significant population differentiation observable, for example, in the Australian lizards Cyclodomorphus praealtus (Koumoundouros et al., 2009) and Egernia species (Chapple et al., 2005), and the endangered mountain pygmy possum (Mitrovski et al., 2007), often explained by lack of suitable habitat between alpine areas. This is clearly not the case in the alpine Poa. ...
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Background and AimsWhile molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone.Methods Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses.Key ResultsSpecies tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5-1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group.Conclusions The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.
... The protection of seminatural open fields in altitude (i.e., highest life zones) is crucial for preserving natural systems and biodiversity. But, among altitudinal biodiversity, some species considered are early indicators of how ecosystems respond to climate change and land use (Koumoundouros et al., 2009). As prediction of habitat trend is complex, observation of these high-altitude sentinel species should inform our conservation policies. ...
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In Europe, the Quaternary is characterized by climatic fluctuations known to have led to many cycles of contraction and expansion of species geographical ranges. In addition, during the Holocene, historical changes in human occupation such as colonization or abandonment of traditional land uses can also affect habitats. These climatically or anthropically induced geographic range changes are expected to produce considerable effective population size change, measurable in terms of genetic diversity and organization. The rock ptarmigan (Lagopus muta) is a small-bodied grouse occurring throughout Northern hemispheric arctic and alpine tundra. This species is not considered threatened at a continental scale, but the populations in the Pyrenees are of concern because of their small population size, geographical isolation and low genetic diversity. Here, we used 11 microsatellites to investigate genetic variations and differentiations and infer the overall demographic history of Pyrenean rock ptarmigan populations. The low genetic variability found in these populations has been previously thought to be the result of a bottleneck that occurred following the last glacial maximum (i.e., 10 000 years ago) or more recently (i.e., during the last 200 years). Our results clearly indicate a major bottleneck affecting the populations in the last tenth of the Holocene. We discuss how this decline can be explained by a combination of unfavorable and successive events that increased the degree of habitat fragmentation.Heredity advance online publication, 10 July 2013; doi:10.1038/hdy.2013.62.
... These same species are often the focus of conservation planning efforts; the negative synergy of climate change along with other stressors such as fragmentation must be a key consideration in conservation designs (Hannah et al., 2005). Climate change can increase levels of fragmentation (Kourmoundouros et al., 2009) and fragmentation can exacerbate climate change effects when it results in barriers preventing species from tracking shifting preferred climate envelopes (Araújo et al., 2004). Our analysis here demonstrates a mechanistic approach, tying climate sensitivity to demographic responses to climate and fragmentation patterns for assessing the impacts of climate change for a narrow endemic species. ...
Article
a b s t r a c t Bioclimatic models aimed assessing a species' sensitivity to climate change incorporate mean shifts in cli-mate variables; however the more acute threat to the persistence of species may result from increased frequency of extreme climatic events, including increased duration and severity of droughts. Here we assess climate-change sensitivity using niche modeling that unlike bioclimatic modeling incorporates both climate variables as well as other habitat features that constrain a species' distribution. We analyzed the effects of potential increases in drought frequency for an endangered, sand dune-restricted lizard, a species restricted to a narrowly occurring substrate and so unable to move up-slope or pole-ward to track climate shifts. Our niche modeling results indicated only minor losses to the area of suitable niche space at lower levels of modeled climate change; at the most severe climate shifts we tested the area of suitable niche space reduced by slightly more than 50%. However, extrapolating the potential impacts of reduced rainfall on drought periodicity and intensity showed a more immediate and acute impact on the lizard's populations. Drought duration projections coupled with landscape fragmentation resulted in rapid losses of suitable niche space, beginning in the more arid portion of the lizard's range and extending into more moderate climate areas. Although there is greater uncertainty associated with the impacts of climate change on drought periodicity than with shifts in mean conditions, our results show a greater potential for droughts to negatively impact species' resilience to such changes.
... Species restricted to wet forests and alpine areas in southeastern Australia show strong molecular divergence between patches indicating long-term isolation, for example, the plants Eucalyptus nitens (Byrne & Moran, 1994), E. regnans (Nevill et al., 2010), Lagarostrobos franklinii (Clark & Carbone, 2008), the mammal Burramys parvus (Osborne et al., 2000;Mitrovski et al., 2007), and the lizard Cyclodomorphus praealtus (Koumoundouros et al., 2009). At Tallaganda in the Great Dividing Range, multiple taxa of springtails and flatworms show spatially congruent patterns in the face of impacts at multiple time scales since the Pliocene (Garrick et al., 2004(Garrick et al., , 2007(Garrick et al., , 2008Sunnucks et al., 2006). ...
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Aim The mesic biome, encompassing both rain forest and open sclerophyllous forests, is central to understanding the evolution of Australia’s terrestrial biota and has long been considered the ancestral biome of the continent. Our aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota. We examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data. In doing so, we increase understanding of the mesic biota and highlight data deficiencies and fruitful areas for future research.
... Because the chloroplast is maternally inherited in most angiosperms, these results suggest a smaller neighborhood for seed dispersal than for pollen dispersal. The Australian alpine zone occurs across small, relatively isolated 'sky islands', and strong spatial genetic structure has been detected in Australian alpine and montane lizards [70,73,74]. However, it is perhaps not surprising that these alpine grasses lack spatial genetic structure with nuclear markers: they are wind-pollinated, and high population connectivity has been documented in one Poa species across mountaintops approximately 8 kilometres apart [75]. ...
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Abstract Background Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. Results Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability. We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at
... This study highlights the particular threats encountered by alpine species that are often locally endemic and restrained to suitable mountainous habitat (see other reptile examples such as Iberolacerta bonnali, Crochet et al. 2003;Cyclodomorphus praealtus, Koumoundouros et al. 2009). As other species confined to sky islands (Browne and Ferree 2007;Holycross and Douglas 2007;Koumoundouros et al. 2009), French populations of the Orsini's viper appear geographically and genetically isolated from each others with low dispersal capability and thus should be considered as separate conservation units (Moritz 1994;Palsboll et al. 2006). Moreover, alpine species are usually physiologically adapted to cold climates (Osborne et al. 2000) and therefore particularly sensitive to temperature increases (Callaghan et al. 2004). ...
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The Orsini’s viper (Vipera ursinii) is one of the most threatened snakes in Europe due to its highly fragmented distribution and specific open environment (steppic habitat) requirement. French populations are isolated on top of mountain massifs of the southern Prealps/Alps. Mitochondrial sequences (cytochrome b) and 6 microsatellite loci have been used to estimate the levels of genetic diversity and isolation within and among 11 French fragmented populations (a total of 157 individuals). Eleven cytochrome b haplotypes with a limited divergence were observed (mean divergence between haplotypes: 0.31%). However, we detected considerable genetic differentiation among populations (global FST = 0.76 and 0.26 for mitochondrial and nuclear DNA, respectively). Results indicate that 3 populations possibly went through a bottleneck and 1 population showed low genetic diversity compared with the others. Although a significant isolation by distance was detected for both markers, strong differentiation was also observed between geographically close populations, probably due to the ragged landscape that constitutes a serious barrier to gene flow owing to the limited dispersal capability of the viper. Despite some discrepancies between the 2 markers, 8 Management Units have been identified and should be considered for future management projects.
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• The fragile alpine freshwater ecosystems of Australia are threatened by historic land use and projected climate change, yet little is known about the fauna of these environments. The aim of this study was to analyse the phylogeography of two important components of this ecosystem, an amphipod (Neoniphargus) and an isopod (Coluboltelson), to determine the potential impacts of environmental change on these crustaceans. • DNA sequences were generated for the mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 28S ribosomal RNA (28S) of 229 amphipods and 153 isopods from 19 sites across seven creeks in the Bogong High Plains, Victoria, Australia. Phylogenetic analyses were undertaken to define evolutionary significant units (ESUs), and population genetic structure was examined. • Analyses of both markers found deep divergences in both taxa, leading to the definition of six amphipod and two isopod ESUs, within both Neoniphargus and Colubotelson. The majority of amphipod ESUs exhibited highly restricted distributions, with essentially no gene flow between sites, even within the same creeks, consistent with the Death Valley Model of population connectivity. By contrast, both isopod ESUs had overlapping distributions across the entire sample area and exhibited some highly limited population connectivity among sites in adjacent headwaters, consistent with the Headwater Model. • This study suggests that there is a high level of undiscovered biodiversity within Australian alpine aquatic invertebrates. The highly limited population structure, and restricted distributions have important consequences for the conservation of the headwaters of Australia's largest river system. These findings indicate that habitat loss and/or fragmentation associated with environmental change will result in biodiversity reductions, with species unlikely to shift their ranges in response to future climate change, or recover rapidly from localised extinction events.
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Thesis (M.A.)--Dept. of Sociology and Anthropology, Concordia University, 1999. Includes bibliographical references (leaves 81-85). "April 1999" Microfiche.
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Comparison of mitochondrial DNA variation among populations of three endemic lizard species in Australia's Wet Tropics rainforest reveals clear evidence of population-level response to Pleistocene rainforest contraction and subsequent expansion. This pattern is repeated in two separate rainforest regions (natural replicates), between which populations have been separated for several million years. Despite evidence for isolation in rainforest refugia, historically reduced effective population size, and recent range expansion, little or no detectable phenotypic evolution has occurred among populations, even those isolated for several million years. These observations suggest that long-term isolation per se, even when combined with major reductions in population size and opportunities for drift and founder effects, is unlikely to be the primary process driving phenotypic divergence and speciation of rainforest vertebrates.
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As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
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Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
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Populations may, during their evolutionary history, go through drastic changes in population size due to bottlenecks or founder events upon colonization of new areas. This involves a subsample of haplotypes, causing the allele frequencies to be different from the original population. In addition, the period of recovery after a bottleneck can be of considerable length. If reproduction is unequal among individuals but random with regard to haplotype, large deviations from the patterns expected in a stable population may result. By means of computer simulation, I have analysed the patterns arising when populations undergo bottlenecks and then slowly recover, and used two new statistical tests for the detection of the bottleneck. A test based on the variance of the relative frequency of haplotypes had generally high power even at low sample size (n=25). This statistic was most powerful after very strong bottlenecks and lost power with increasing propagule size. A test based on the variance of the pairwise differences shows slightly less power. As expected, power was reduced when migration into the founder population was allowed from the source population. This suggests that the test is particularly suited for detecting relatively recent and strong bottlenecks, and thus may be a valuable tool for identifying population events on a fine temporal scale, such as colonisations after the last glaciation.
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Since the idea of the Pliocene Kosciusko Uplift in the Southeastern Highlands of Australia was first introduced, there has been considerable debate about the validity of this Cenozoic uplift event. Until the mid 1990s, most researchers argued that most highland relief was present by the Cretaceous. Since the late 1990s, there has been a paradigm shift that extensive young Cenozoic uplift created much of the high relief. In this paper, we synthesise Cenozoic stratigraphic and structural data from the East Victoria Highlands to assess the timing and origin of uplift. New high-resolution radar topography data indicate extensive east-northeast- and northeast-trending vertical and horizontal fault block displacement of the Cenozoic volcanic and sedimentary paleovalley infill. We suggest that regional uplift and exhumation of the East Victoria Highlands took place along these faults, initiated during the Late Eocene to Early Oligocene, and movements continue to the present day. By a combination of block faulting and epeirogenic uplift the divide migrated 40 km north reaching the present position by Pliocene time. Paleocurrent, lateral stream and magnetic basaltic valley flow directions indicate northward paleoflow directions for many of the Eocene - Oligocene valleys even those south of the present divide. Paleovalleys close to the Gippsland Basin show southward flow directions. The uplift that began in the Eocene causing valley cut and infill, eroded an Early Cenozoic paleoplain surface. Remnants of Late Eocene to Oligocene ligneous sediments are preserved as sub-basaltic, lowland valley, fluvio-lacustrinal sediment on this surface. Three large low-gradient paleodrainage systems that begin south of the present divide flowed north over 100 km to the Murray Basin where they are overlain by younger sediments. In contrast, paleodrainage systems flowing south from the present coastal escarpment to Gippsland, were shorter and steeper. The similarities of palynofacies of this infill to the adjacent basins suggest the valleys were low-relief/low-altitude paleodrainage systems that extended over the East Highlands. Based on our palynology results from Mt Hotham (present-day height 1800 m), previous macrofossil estimates of 800 m maximum Eocene relief could be overestimates of the paleo-height. Due to Cenozoic uplift, the strata (where present) are preserved as hilltop deposits and flows tilted away from the present divide. The Late Eocene to Pliocene uplift is probably primarily responsible for the topographic relief of the present East Victoria Highlands, is of the order of several hundreds of metres to a kilometre, and commenced in the Late Eocene at a divide closer to the Gippsland Basin than at present. This uplift continues to the present day as shown by the active seismicity in the area.
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A molecular phylogeny of the Spizaetus cirrhatus complex is presented in this study, based on two sections of the mitochondrial genome: partial sequences of the cytochrome b gene and of the control region (CR). The topologies derived from the two sequences are in agreement. Within S. cirrhatus distances are rather low (0–1.5% in cytochrome b). Among the cirrhatus subspecies the island taxa floris, vanheurni and andamanensis form distinct haplogroups in the CR trees, conforming to the earlier subspecific divisions which were based on morphological characters. On the other hand, the most widespread subspecies, limnaeetus, does not represent a monophyl-etic group in the gene trees and its haplogroups do not cluster according to geographic affinities. An unambiguous resolution of relationships among haplotypes and haplogroups, respectively, was not achieved, suggesting a more recent radiation of this group of hawk-eagles in the course of the last ice ages. Concerning the outgroup taxa Spizaetus philippensis and Spizaetus lanceolatus, our data indicate a clear genetic distinction between the two subspecies S. p. philippensis and S. p. pinskeri, suggesting that they should be treated as distinct species. Yet the phylogenetic relationships of the three outgroup taxa with respect to S. cirrhatus are ambiguous in our trees. The taxonomic consequences of applying different species concepts (BSC, PSC) are discussed. The species concept chosen would result in different conservation strategies.
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We describe two methods for detecting population expansions based on variation at unlinked microsatellite loci. The tests were first used in a study of human demographic history that showed evidence for a Paleolithic human population expansion in Africa. Here, we provide a simple recipe for applying the tests to other data sets and describe the power of the tests as a function of the sample size, number of loci, mutation rate, diploid population size N 0 , and time since expansion. An important property of the tests is that as long as the population doubles at least once every 0.1N 0 generations, where N 0 now represents the pre-expansion population size, and the overall factor of expansion is sufficiently large, the signal of growth will be nearly identical to one generated by a sudden and massive expansion. This greatly simplifies the mathematical modeling necessary to evaluate the test results but also means that many patterns of growth will be indistinguishable using the tests. A second conclusion from our analysis is that the tests show different sensitivities to specific deviations from the biological and demographic models. Hence, more information can be garnered from the two tests taken together than from either alone.
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Aim  Many plants occurring on the isolated mountain peaks of Africa have their closest relatives in very remote areas, even in temperate Europe and Asia. Their biogeographical history is poorly understood. The Afro-montane element of the primarily Eurasian genus Lychnis is a typical example of such a disjunction. Here, we aim to reconstruct the phylogeny of the Afro-montane endemics of Lychnis and to infer the history of immigration into Africa and of the subsequent dispersal and speciation.Location  The Afro-montane representatives of Lychnis occur in Ethiopia, Kenya, Tanzania, Uganda, Rwanda, Burundi, the Democratic Republic of Congo, Cameroon, and Nigeria.Methods  Silica-dried plant materials collected in Ethiopia in 2004 as well as herbarium material were used for DNA extractions. We used parsimony analysis of nucleotide data from the rps16 intron and psbE-petL region in plastids, and the internal transcribed spacer (ITS) and a region spanning exon 18–24 in the second largest subunit of RNA polymerase II (RPB2) from the nucleus. DAPI-flow cytometry was used to determine relative genome size and to infer polyploidization events.Results  Monophyly of the Afro-montane Lychnis with the Eurasian diploid L. flos-cuculi resolved as sister was strongly supported by the phylogenetic analyses. The Afro-montane group was further divided into two strongly supported groups correlated with DNA ploidy levels. The relative genome size was species-specific except for L. abyssinica, which had two genome-size variants.Main conclusions  Our results demonstrate that the biogeographical history of the Afro-montane Lychnis has been highly dynamic, including polyploidization and both old and recent long-distance dispersal events, even between Eastern and West Africa. The ancestor is inferred to have immigrated once from Eurasia via the Arabian Peninsula to the Ethiopian highlands. Divergence in the lineage containing diploid taxa was followed by several dispersals from Ethiopia to the Eastern and Western Rift Mountains, and recently to West Africa. Divergence of the lineage including the tetraploid L. crassifolia may have taken place in Ethiopia, from where it dispersed to the Eastern and Western Rift Mountains; alternatively, it may have taken place in the Eastern Rift Mountains, followed by dispersal from there to the Western Rift Mountains and then to Ethiopia.
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Recent years have seen a debate over various methods that could objectively prioritize conservation value below the species level. Most prominent among these has been the evolutionarily significant unit (ESU). We reviewed ESU concepts with the aim of proposing a more unified concept that would reconcile opposing views. Like species concepts, conflicting ESU concepts are all essentially aiming to define the same thing: segments of species whose divergence can be measured or evaluated by putting differential emphasis on the role of evolutionary forces at varied temporal scales. Thus, differences between ESU concepts lie more in the criteria used to define the ESUs themselves rather than in their fundamental essence. We provide a context-based framework for delineating ESUs which circumvents much of this situation. Rather than embroil in a befuddled debate over an optimal criterion, the key to a solution is accepting that differing criteria will work more dynamically than others and can be used alone or in combination depending on the situation. These assertions constitute the impetus behind adaptive evolutionary conservation.
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We used an enrichment technique to isolate 18 novel di and tri microsatellites for the socially monogamous lizard Tiliqua rugosa. These loci were amplified in conjunction with previously described loci in two and three PCR multiplexes for T. rugosa and the endangered T. adelaidensis, respectively. The loci were highly polymorphic in both species, exhibiting between 2 and 32 alleles with observed heterozygosity ranging from 0.43 to 0.96. These markers will be useful for population-level analyses and can contribute to a genetic foundation for conservation strategies for the endangered T. adelaidensis.
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Uses a model of snow-cover duration, an observed climate data set for the Australian alpine area, and a set of regional climate-change scenarios to assess quantitatively how changes in climate may affect snow cover in the Australian Alps. The model provides a reasonable simulation of the sensitivities of snow-cover duration to changes in temperature and precipitation in the Australian Alps. The input climate data are then modified in line with scenarios of regional climate change for the years 2030 and 2070. Under the best case scenario for 2030, simulated average snow-cover duration and the frequency of years of more than 60 days cover decline at all sites considered. However, at the higher sites (eg more than 1700 m) the effect is not very marked. For the worst case scenario, a much more dramatic decline in snow conditions is simulated. At higher sites, simulated average snow cover duration rougly halves by 2030 and approaches zero by 2070. At lower sites (around 1400 m), near zero average values are simulated by 2030 (compared to durations of around 60 days for current climate).
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Climate change during the Quaternary played an important role in the differentiation and evolution of plants. A prevailing hypothesis is that alpine and arctic species survived glacial periods in refugia at the periphery of glaciers. Though the Rocky Mountains, south of the southernmost extent of continental ice, served as an important glacial refuge, little is known about how climate cycles influenced populations within this region. We inferred the phylogeography of Sedum lanceolatum (Crassulaceae) within the Rocky Mountain refugium to assess how this high-elevation plant responded to glacial cycles. We sequenced 884 base pairs (bp) of cpDNA intergenic spacers (tRNA-L to tRNA-F and tRNA-S to tRNA-G) for 333 individuals from 18 alpine populations. Our highly variable markers allowed us to infer that populations persisted across the latitudinal range throughout the climate cycles, exhibited significant genetic structure, and experienced cycles of range expansion and fragmentation. Genetic differentiation in S. lanceolatum was most likely a product of short-distance elevational migration in response to climate change, low seed dispersal, and vegetative reproduction. To the extent that Sedum is a good model system, paleoclimatic cycles were probably a major factor preserving genetic variation and promoting divergence in high-elevation flora of the Rocky Mountains.
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This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.
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Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
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We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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Examines the form and frequency of 3 types of change in mtDNA: base substitution, length variation and sequence rearrangement. Knowledge of molecular processes allows informed use of mtDNA variation in evolutionary studies.-P.J.Jarvis
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We describe two methods for detecting population expansions based on variation at unlinked microsatellite loci. The tests were first used in a study of human demographic history that showed evidence for a Paleolithic human population expansion in Africa. Here, we provide a simple recipe for applying the tests to other data sets and describe the power of the tests as a function of the sample size, number of loci, mutation rate, diploid population size N0, and time since expansion. An important property of the tests is that as long as the population doubles at least once every 0.1N0 generations, where N0 now represents the pre-expansion population size, and the overall factor of expansion is sufficiently large, the signal of growth will be nearly identical to one generated by a sudden and massive expansion. This greatly simplifies the mathematical modeling necessary to evaluate the test results but also means that many patterns of growth will be indistinguishable using the tests. A second conclusion from our analysis is that the tests show different sensitivities to specific deviations from the biological and demographic models. Hence, more information can be garnered from the two tests taken together than from either alone.
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Alpine environments are characterized by short, cold, unpredictable growing seasons. Outside of the Arctic this growing season is characterized by cold nights as well. Alpine plant adaptations are much like those of the Arctic in morphological and physiological characteristics. However, they appear to acclimate metabolically to changes in temperature more easily than do arctic ecotypes. In fact, almost all representatives of arctic-alpine species are ecotypically different from their congeners in the Arctic. This is particularly true in reproduction and metabolism, the real heart of adaptation to cold alpine environments. While there are relatively ancient alpine plant taxa, the accelerated rise of new mountain ranges in late Pliocene and Pleistocene times has led to new floristic aggregations in alpine vegetations by migration and adaptive radiation. Fluctuations in Pleistocene glaciations have alternately allowed migrations and blocked them. Interglacial refugia may be more important than glacial refugia in consolidating evolutionary changes in alpine taxa which evolve in response to decreasing temperatures, increasing light intensities, and in some cases to increasing drought stress.
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Establishment of forest trees into subalpine grasslands near Mt. Hotham, southeast Australia, was quantified in 1998 across long-established forest-grassland boundaries in belt transects at four sites. Although the grasslands varied in their dominant species and groundlayer biomass, tree encroachment (principally by Eucalyptus pauciflora) occurred at all sites. Tree encroachment is a recent and synchronous event; all invading saplings were ≤31-yr-old and the majority (54%) established between 1991 and 1995. Most sapling establishment (66%) occurred within 5 m of the forest-grassland boundary where the number of plants present was positively associated with the amount of overhanging tree cover at three of the four sites. No correlation between encroachment and groundcover type or biomass, however, was found at any site. Some of the recently established plants are now small trees (1-8 m in height) and have become reproductive, indicating that establishment in grasslands is successful, making ecotone shifts possible. Any changes in boundary position, however, will be slow given the limited distance that trees established from the forest edge. Tree encroachment near Mt. Hotham is likely the outcome of small-scale (e.g., regeneration microsite) and landscape-scale (e.g., climate, grazing) processes that require further clarification.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
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... There also appears to be a major phylogeographical break within E. whitii occurring in ... Akaike Information Criterion (AIC) to select the most appropriate model of molecular evolution for ... We tested a range of hypotheses regarding the systematics and biogeographical patterns of ...
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Conservation requires the accurate targeting of resources together with information on population processes. Molecular phylogenies can potentially contribute in both areas. Interspecific molecular phylogenies can identify clades undergoing rapid diversification or extinction and can assess the contribution of individual lineages to overall genetic diversity. Whether and how this should translate to conservation priorities is open to debate. Within species, molecular phylogenies along with information on allele frequencies can be used to identify evolutionarily significant population units or areas. In relation to population processes, molecular phylogenies may provide a perspective on population growth and connectivity over evolutionary time. As threatened species typically have undergone rapid changes in population size and/or migration rate, phylogeny-based estimates may be misleading about contemporary population processes. However, the comparison between historical and current estimates may identify significant changes to long-term trends, thus identifying population in need of urgent management. This information can potentially suggest strategies for managing declining or fragmented species, but this requires further theoretical and experimental study.
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Sequence data from a 597-base pair region of the mitochondrial DNA control region and data for 19 presumed allozyme loci were used to examine genetic structure and to detect gene flow among populations of southern red-backed voles (Myodes gapperi, formerly known as Clethrionomys gapped) inhabiting spruce-fir “sky-islands” in the southern Appalachians. Allozyme data showed a significant heterozygote deficiency for most populations. Average individual heterozygosity varied among populations from 1.75% to 16.78% (X̄ ± SE = 8.63% ± 2.03%). Rvalues between any 2 sites ranged from 0.100 to 0.517 (X̄ ± SE = 0.296 ± 0.026), with a significant metapopulation FST value = 0.599. Nei's genetic distances (based on allozyme data) among spruce-fir habitats ranged from 0.037 to 0.310 (X̄ ± SE = 0.139 ± 0.079). Analysis of molecular variance permitted determination of the extent of geographic subdivision of mitochondrial haplotypes for 3 hierarchically organized sampling regimes: 14 high-altitude sample sites; 7 spruce-fir islands within which the sample sites are located; and whether sample sites were located south or north of the dominant, low-altitude barrier, the French Broad River. Genetic variation among groups and ウST values were highly significant for all sampling regimes, indicating significant population structure at all hierarchical levels tested. Mantel's general regression test indicated that gene flow and genetic relationships fit an isolation-by-distance model. Since the Pleistocene, gene flow within the metapopulation of M. gapperi appears to have declined as a result of increasing distances between habitat islands and because of population bottlenecks.
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The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
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SUMMARY AND CONCLUSIONS1The major part of Broom's original collection of specimens of Burramys parvus Broom has been re-examined with the acetic acid technique.2Additional information thus acquired makes it certain that Burramys parvus does not belong within the Macropodidae, nor is it ancestral to them.3Resemblances to Hypsiprymnodon moschatus are the result of convergence, and suggested affinities with Thylacoleo appear to be without adequate foundation.4Burramys parvus has features in common with several genera of Phal-angerinae, in particular with Eudromicia, Cercaertus, and Petaurus and should be included in this subfamily instead of being placed in a separate monotypic subfamily.5Those figured specimens of the species described by Broom from the Wombeyan Caves, New South Wales, which are at present in the Australian Museum, Sydney, must be presumed to be the types.
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This review summarizes recent research in Australia on: (i) climate and geophysical trends over the last few decades; (ii) projections for climate change in the 21st century; (iii) predicted impacts from modelling studies on particular ecosystems and native species; and (iv) ecological effects that have apparently occurred as a response to recent warming. Consistent with global trends, Australia has warmed ~ 0.8 C over the last century with minimum temperatures warming faster than maxima. There have been significant regional trends in rainfall with the northern, eastern and southern parts of the continent receiving greater rainfall and the western region receiving less. Higher rainfall has been associated with an increase in the number of rain days and heavy rainfall events. Sea surface temperatures on the Great Barrier Reef have increased and are associated with an increase in the frequency and severity of coral bleaching and mortality. Sea level rises in Australia have been regionally variable, and considerably less than the global average. Snow cover and duration have declined significantly at some sites in the Snowy Mountains. CSIRO projections for future climatic changes indicate increases in annual average temperatures of 0.4–2.0 C by 2030 (relative to 1990) and 1.0–6.0 C by 2070. Considerable uncertainty remains as to future changes in rainfall, El Niño Southern Oscillation events and tropical cyclone activity. Overall increases in potential evaporation over much of the continent are predicted as well as continued reductions in the extent and duration of snow cover. Future changes in temperature and rainfall are predicted to have significant impacts on most vegetation types that have been modelled to date, although the interactive effect of continuing increases in atmospheric CO 2 has not been incorporated into most modelling studies. Elevated CO 2 will most likely mitigate some of the impacts of climate change by reducing water stress. Future impacts on particular ecosystems include increased forest growth, alterations in competitive regimes between C3 and C4 grasses, increasing encroachment of woody shrubs into arid and semiarid rangelands, continued incursion of mangrove communities into freshwater wetlands, increasing frequency of coral bleaching, and establishment of woody species at increasingly higher elevations in the alpine zone. Modelling of potential impacts on specific Australian taxa using bioclimatic analysis programs such as BIOCLIM consistently predicts contraction and/or fragmentation of species' current ranges. The bioclimates of some species of plants and vertebrates are predicted to disappear entirely with as little as 0.5–1.0 C of warming. Australia lacks the long-term datasets and tradition of phenological monitoring that have allowed the detection of climate-change-related trends in the Northern Hemisphere. Long-term changes in Australian vegetation can be mostly attributed to alterations in fire regimes, clearing and grazing, but some trends, such as encroachment of rainforest into eucalypt woodlands, and establishment of trees in subalpine meadows probably have a climatic component. Shifts in species distributions toward the south (bats, birds), upward in elevation (alpine mammals) or along changing rainfall contours (birds, semiarid reptiles), have recently been documented and offer circumstantial evidence that temperature and rainfall trends are already affecting geographic ranges. Future research directions suggested include giving more emphasis to the study of climatic impacts and understanding the factors that control species distributions, incorporating the effects of elevated CO 2 into climatic modelling for vegetation and selecting suitable species as indicators of climate-induced change.
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Abstract Australian alpine ecosystems are expected to diminish in extent as global warming intensifies. Alpine vegetation patterns are influenced by the duration of snow cover including the presence of snowdrifts in summer, but there is little quantitative information on landscape-scale relationships between vegetation patterns and the frequency of occurrence of persistent summer snowdrifts in the Australian alps. We mapped annual changes in summer snowdrifts in the Kosciuszko alpine region, Australia, from Landsat TM images and modelled the frequency of occurrence of persistent summer snowdrifts from long-term records (1954–2003) of winter snow depth. We then compared vegetation composition and structure among four classes that differed in the frequency of occurrence of persistent summer snowdrifts. We found a curvilinear relationship between annual winter snow depth and the area occupied by persistent snowdrifts in the following summer (r2 = 0.9756). Only 21 ha (0.42% of study area) was predicted to have supported summer snowdrifts in 80% of the past 50 years, while 440 ha supported persistent summer snow in 10% of years. Mean cover and species richness of vascular plants declined significantly, and species composition varied significantly, as the frequency of summer snow persistence increased. Cushion plants and rushes were most abundant where summer snowdrifts occurred most frequently, and shrubs, grasses and sedges were most abundant in areas that did not support snowdrifts in summer. The results demonstrate strong regional relationships between vegetation composition and structure and the frequency of occurrence of persistent summer snowdrifts. Reductions in winter snow depth due to global warming are expected to lead to substantial reductions in the extent of persistent summer snowdrifts. As a consequence, shrubs, grasses and sedges are predicted to expand at the expense of cushion plants and rushes, reducing landscape vegetation diversity. Fortunately, few vascular plant species (e.g. Ranunculus niphophilus) appear to be totally restricted to areas where summer snow occurs most frequently. The results from this study highlight potential indicator species that could be monitored to assess the effects of global warming on Australian alpine environments.
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There has a been a resurgence of debate on whether the Pleistocene glaciations inhibited speciation. This study tests a model of Pleistocene speciation, estimating the phylogenetic relationships and divergence times of 10 species of montane grasshoppers, genus Melanoplus, using 1300 bp of the mitochondrial gene cytochrome oxidase I (COI). Based on average pairwise distances (corrected for multiple substitutions using Kimura's two-parameter model), all species appear to have originated within the Pleistocene. Sequence divergences between species are less than 4%, corresponding to divergence times less than 1.7 million years ago. Branching patterns among the species suggest that speciation was associated with more than one glacial-interglacial cycle. A likelihood-ratio test rejected a model of simultaneous species origins, the predicted branching pattern if species arose from the fragmentation of a widespread ancestor. These grasshoppers live in an area that was previously glaciated and, as inhabitants of the northern Rocky Mountain sky islands, underwent latitudinal and probably altitudinal shifts in distribution in response to climatic fluctuations. Given the repeated distributional shifts and range overlap of the taxa, there most likely has been ample opportunity for population mixing. However, despite periodic glacial cycles, with more than 10 major glaciations over the past million years and climatic fluctuations over as short a time scale as 103 to 104 years, the dynamic history of the Pleistocene did not preclude speciation. Although relationships among some taxa remain unresolved, these grasshopper species, even with their recent origins, exhibit genetic coherence and monophyletic or paraphyletic gene trees. The frequency of glacial cycles suggests that the speciation process must have been extremely rapid. These species of grasshoppers are morphologically very similar, differing primarily in the shape of the male genitalia. These characters are posited to be under sexual selection, may play an important role in reproductive isolation, and are known to diverge rapidly. This suggests the rapidity of evolution of reproductive isolation may determine whether species divergences occurred during the Pleistocene glaciations.
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Twenty-five years of extensive water temperature data show regionally coherent warming to have occurred in Alpine rivers and streams at all altitudes, reflecting changes in regional air temperature. Much of this warming occurred abruptly in 1987/1988. For brown trout populations, the warming resulted in an upward shift in thermal habitat that was accelerated by an increase in the incidence of temperature-dependent Proliferative Kidney Disease at the habitat's lower boundary. Because physical barriers restrict longitudinal migration in mountain regions, an upward habitat shift in effect implies habitat reduction, suggesting the likelihood of an overall population decrease. Extensive brown trout catch data documenting an altitudinally dependent decline indicate that such a climate-related population decrease has in fact occurred. Our analysis employs a quantitatively defined reference optimum temperature range for brown trout, based on the sinusoidal regression of seasonally varying field data.
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Aim  We inferred the phylogeography of the alpine butterfly Colias meadii Edwards (Pieridae) and compared its genetic structure with that of another high elevation, co-distributed butterfly, Parnassius smintheus Doubleday (Papilionidae), to test if the two Rocky Mountain butterflies responded similarly to the palaeoclimatic cycles of the Quaternary.Location  Specimens were collected from 18 alpine sites in the Rocky Mountains of North America, from southern Colorado to northern Montana.Methods  We sequenced 867 and 789 nucleotides of cytochrome oxidase I from an average of 19 and 20 individuals for C. meadii and P. smintheus, respectively, from each of the same 18 localities. From the sequence data, we calculated measures of genetic diversity within each population (H, θ), genetic divergence among populations (FST), and tested for geographic structure through an analysis of molecular variance (amova). Population estimates were compared against latitude and between species using a variety of statistical tests. Furthermore, nested clade analysis was implemented to infer historic events underlying the geographic distribution of genetic variation in each species. Then, we compared the number of inferred population events between species using a nonparametric Spearman's rank correlation test. Finally, we ran coalescent simulations on each species’ genealogy to test whether the two species of Lepidoptera fit the same model of population divergence.Results  Our analyses revealed that: (1) measures of within-population diversity were not correlated with latitude for either species, (2) within-site diversity was not correlated between species, (3) within a species, nearly all populations were genetically isolated, (4) both species exhibited significant and nearly identical partitioning of genetic variation at all hierarchical levels of the amova, including a strong break between populations across the Wyoming Basin, (5) both species experienced similar cycles of expansion and contraction, although fewer were inferred for C. meadii, and (6) data from both species fit a model of three refugia diverging during the Pleistocene.Main conclusions  While our findings supported a shared response of the two butterfly species to historic climate change across coarse spatial scales, a common pattern was not evident at finer spatial and temporal scales. The shared demographic history of the two species is consistent with an expanding–contracting archipelago model, suggesting that populations persisted across the geographic range throughout the climate cycles, experiencing isolation on ‘sky islands’ during interglacial periods and becoming connected as they migrated down-slope during cool, wet climates.
Article
DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO-CHECKER is WINDOWS(R)-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO-CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
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It has been predicted that enhanced greenhouse climate change will modify the global climate and consequently cause large-scale changes to the distribution of flora and fauna. This study examined the potential effect of enhanced greenhouse climate change on the distribution of 42 species of fauna of south-eastern Australia. The best available information regarding faunal distributions and predictive models for bioclimatic ranges was used in conjunction with the accepted enhanced greenhouse climate scenarios for 1990. More recent developments that refine the potential climatic changes are discussed in relation to the analysis.The 42 species of fauna were selected from the major Victorian bioclimatic regions and ecosystems and from species considered most at risk from enhanced greenhouse climate change. Most were species with a threatened conservation status. The results indicate that 41 undergo a reduction in bioclimatic range in response to climatic warming, the most extreme response being the extinction of bioclimatic range. A broadscale subcontinental analysis of the potential effects on faunal distribution is presented.
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Genetic studies in endangered species have become widespread in the past decade, and with new information from various genome projects, new applications and insights are forthcoming. Generally, neutral variants are used for conservation applications, and when combined with highly variable loci and/or many more markers, these approaches should become much more informative. Conservation genetics is also concerned with detrimental and adaptive variation, which are more difficult to identify and characterize; however, the ability to predict the extent of such variation might become more successful and applied in future conservation efforts. Neutral variants might be used to identify adaptive variants, but the overlay of different mutational processes and selective regimes suggests that extreme caution should be used in making such identifications.
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w riting in the first issue of TREE, Ryder' brought the term 'Evolution- arily Significant Unit' (ESU) to the atten- tion of a broad audience of ecologists and evolutionary biologists. The ESU concept was developed to provide a rational basis for prioritizing taxa for conservation effort (e.g. captive breeding), given that resources are limited and that existing taxonomy may not adequately reflect underlying genetic diversity*. With the explicit recognition of the genetic com- ponent of biodiversity in conservation legislation of many countries and in the Convention on Biological Diversity, the ESU concept is set to become increas- ingly significant for conservation of natural as well as captive populations. However, the ESU remains poorly de- fined, both conceptually and operation- ally. Most definitions suggest than an ESU should be geographically discrete, but genetic criteria range from significant di- vergence of allele frequencies3 through some level of genetic distance' to congru- ently structured phylogenies among gene+. Several authors have argued that an ESU should display concordant divergence for both molecular and non- molecular traitG6. Although all are try- ing to achieve the same end, it seems that the operational definitions vary according to the biological and legislat- ive context. The purpose of this essay is to revisit the ESU concept in relation to recent developments in molecular popu- lation genetics. The suggested defi- nitions and criteria are not supposed to be proscriptive - rather, the intention is to promote debate on the purpose and practice of using genetic information to define conservation units. Conservation goals: what do we mean by 'significant'?
Article
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