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Understanding what factors drive patterns of genetic diversity is a central aspect of many biological questions, ranging from the inference of historical demography to assessing the evolutionary potential of a species. However, as a larger number of datasets have become available, it is becoming clear that the relationship between the characteristi...
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... tested on their own, most of the 21 factors considered in this study were not significantly related to measures of genetic diversity (at α = 0.05) and did not show strong effect sizes (Tables 2 and 3). ...
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... none were significantly related to measures of genetic di- versity for both the nuclear and mitochondrial markers (Tables 2 and 3). ...
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... of the continuous variables showed significant correlation with at least one of the genetic markers (Table 2). According to the PICS analysis, Population size was only correlated with nuclear DNA genetic diversity. ...
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... corresponds to a null model and descriptions of πR, πO, micR, and micO can be found in the legend of T A B L E 5 Phylogenetic generalized least squares analysis results and their associated sample size in number of species (n) and Pagel's λ value. Descriptions of πR, πO, micR, and micO can be found in the legend of Table 2 ...
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Background
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... Cetaceans are distributed across vastly different ecosystems and might show pronounced genetic structuring despite a significantly reduced molecular substitution rate and long generation times compared with other mammals (McGowen, Grossman, and Wildman 2012;Sosa and Pilot 2023;Sun et al. 2019;Tollis et al. 2019;Vachon, Whitehead, and Frasier 2018). In coastal regions, fine-scale genetic structure appears to be influenced by environmental heterogeneity, and has been reported in harbour porpoises (Phocoena phocoena, Fontaine et al. 2007;Celemín et al. 2023), franciscana dolphins (Pontoporia blainvillei, Mendez et al. 2010;Gariboldi et al. 2016 Barceló et al. 2022) and within the genus Tursiops in particular (Krützen et al. 2004;Natoli et al. 2005;Bilgmann et al. 2007;Tezanos-Pinto et al. 2009;Wiszniewski et al. 2010;Fruet et al. 2014;Pratt et al. 2022;Wittwer et al. 2023). ...
Demographic processes can substantially affect a species' response to changing ecological conditions, necessitating the combined consideration of genetic responses to environmental variables and neutral genetic variation. Using a seascape genomics approach combined with population demographic modelling, we explored the interplay of demographic and environmental factors that shaped the current population structure in Indo‐Pacific bottlenose dolphins ( Tursiops aduncus ) along the Western Australian coastline. We combined large‐scale environmental data gathered via remote sensing with RADseq genomic data from 133 individuals at 19 sampling sites. Using population genetic and outlier detection analyses, we identified three distinct genetic clusters, coinciding with tropical, subtropical and temperate provincial bioregions. In contrast to previous studies, our demographic models indicated that populations occupying the paleo‐shoreline split into two demographically independent lineages before the last glacial maximum (LGM). A subsequent split after the LGM 12—15 kya gave rise to the Shark Bay population, thereby creating the three currently observed clusters. Although multi‐locus heterozygosity declined from north to south, dolphins from the southernmost cluster inhabiting temperate waters had higher heterozygosity in potentially adaptive loci compared to dolphins from subtropical and tropical waters. These findings suggest ongoing adaptation to cold‐temperate waters in the southernmost cluster, possibly linked to distinct selective pressures between the different bioregions. Our study demonstrated that in the marine realm, without apparent physical boundaries, only a combined approach can fully elucidate the intricate environmental and genetic interactions shaping the evolutionary trajectory of marine mammals.
... Frasier 2018;De Kort et al. 2021;Larkin et al. 2023;Segovia-Ramírez et al. 2023). Also, explanatory variables at deep phylogenetic scales often do not capture patterns of genetic variation within individual focal clades (Singhal et al. 2017). ...
... For example, most studies have primarily used mitochondrial evidence, which because of sex-biased dispersal and smaller effective sizes, tend to show more population structure. More generally, mitochondrial diversity in animals weakly predicts variation in nuclear π (see Ellegren and Galtier 2016;Singhal et al. 2017;Vachon, Whitehead, and Frasier 2018). More recent mygalomorph studies using phylogenomic nuclear evidence have emphasised phylogeographic divergence among populations (e.g., Newton et al. 2020;Marsh, Bradford, and Cooper 2023;Monjaraz-Ruedas, Mendez, and Hedin 2023;Starrett et al. 2024;Opatova, Bourguignon, and Bond 2024), rather than measuring both nuclear genomic diversity and differentiation. ...
Although patterns of population genomic variation are well-studied in animals, there remains room for studies that focus on non-model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome-wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within- and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small-bodied taxa. We also predicted greater genetic differentiation in small-bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation-by-distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species-rich animal clade.
... From a conservation perspective, the Irrawaddy dolphin's distribution range has high anthropogenic disturbance due to massive infrastructure development and associated disruptions from agriculture and aquaculture (Duckworth et al., 2012;Hughes, 2017) leading to significant declines in the range and dolphin numbers (Minton et al., 2018). Population declines uncontestably lead to the potential loss of genetic diversity, population fitness and elevated risk of local extinction (Frankham, 2005;Vachon et al., 2018). ...
... However, a dispersal barrier, likely established within the last 3-4 generations, appears to currently disrupt connectivity between SKL and the LGT population. For long-lived species like the Irrawaddy dolphin, a time lag exists between barrier formation and detectable genetic structuring (Vachon et al., 2018;Louis et al., 2021;Budi et al., 2022). The non-significant difference between SKL and IDN population might also be attributed to limited sample size, given the substantial environmental separation. ...
Importance of the work: The decline in numbers of the Irrawaddy dolphin threatens its viability. Genetic data scarcity imperils management decisions. Objectives: To apply microsatellite-based analysis to assess the genetic diversity and population structure of the Irrawaddy dolphin in Thailand and Indonesia. Materials & Methods: Skin and muscle samples were collected from stranded Irrawaddy dolphins in coastal and riverine areas of Thailand (n = 64) and Indonesia (n = 10). Individual DNA was analyzed using 12 microsatellite primers. However, DNA from only 15 individuals from Thailand and five from Indonesia could be successfully amplified. The data obtained were then used to assess population genetic parameters and population structure. Results: A high level of genetic diversity was observed among Irrawaddy dolphin populations in Thailand and Indonesia. In total, 106 alleles were identified across four populations in Thailand and Indonesia, with mean observed heterozygosity (H o) of 0.625 ± 0.048 and an allelic richness of 4.125 ± 0.182. Pairwise population differentiation and discriminant analysis of principal components supported significant population heterogeneity. These findings suggested a population structure within Irrawaddy dolphins across Thailand and Indonesia, contradicting the common assumption of panmixia in marine mammal populations. Main finding: Genotyping data revealed a population substructure within Irrawaddy dolphin populations in Thailand and Indonesia, highlighting potential challenges for their long-term conservation.
... Mitochondrial DNA diversity (mtDNA) appears to be mostly influenced by the range and social structure of the species (Vachon et al. 2018). False killer whales are matrilineal in the sense that both males and females are generally closely grouped with their mothers while both are alive (Baird 2009;Mahaffy et al. 2023). ...
False killer whales (Pseudorca crassidens) are globally distributed cetaceans, often found in deep oceanic waters but occasionally near coastlines. Despite their broad distribution, information on their abundance, genetics, and ecology remains limited. In New Zealand waters, these whales occur year-round, with increased sightings during the warmer months due to the East Auckland Current. This study investigates the genetic diversity and population structure of New Zealand false killer whales using 17 samples collected from 2005 to 2018 in four locations, comparing them to global studies. New Zealand samples revealed four unique haplotypes with low genetic diversity (h = 0.42 ± 0.141; π = 0.29%± 0.002). No genetic differentiation was observed between South Pacific and New Zealand populations (F ST = 0.05 p = 0.1602 F ST = 0.058 p = 0.145). These findings suggest low genetic diversity for New Zealand false killer whales, but within values expected for other cetaceans with matrilineal social structures. The presence of shared haplotypes suggests potential historical or ongoing connections with wider Pacific populations. However, further research is needed due to the short mtDNA-CR fragment analysed and small sample size, which may have resulted in an inability to capture the full extent of the genetic variation. This study contributes to our understanding of this species and its conservation within New Zealand. ARTICLE HISTORY
... Restricted dispersal due to human disturbances and low population numbers make Irrawaddy dolphins in Songkhla Lake and the Lower Gulf of Thailand particularly vulnerable to demographic stochasticity, genetic drift, and inbreeding (Budi et al. 2022), leading to genetic diversity loss, reduced population fitness, and increased risk of local extinction (Ruiz-García et al. 2018;Vachon et al. 2018). Conversely, enhanced dispersal and gene flow among remnant populations within spatially structured metapopulations can potentially mitigate these negative effects. ...
... The apparent absence of genetic structure suggesting a panmictic population could be attributed to the Irrawaddy dolphin's extended generation time and lifespan (Vachon et al. 2018;Louis et al. 2021). These factors may impede allele fixation or loss within populations (Pfennig and Lachance 2022), thereby delaying genetic differentiation. ...
Budi T, Ninwat S, Sakornwimon W, Thongcham K, Phakphien R, Kalaya C, Phavaphutanon J. 2024. Genetic diversity and connectivity of the Irrawaddy dolphin in Southern Thailand: Emphasizing the last fourteen of the Songkhla dolphin status from a microsatellite perspective. Biodiversitas 25: 1729-1735. Irrawaddy dolphin (Orcaella brevirostris Gray, 1866) can be found in diverse aquatic environments, ranging from coastal to brackish water, stretching from the West of Bengal in India to the central part of the Indonesian archipelago. Despite its widespread distribution and flexible habitat tolerance, Irrawaddy dolphins in Songkhla Lake, Southern Thailand, are hypothesized to be isolated and exhibit concerningly low population numbers, threatening their long-term survival. Limited knowledge exists regarding their population genetics status. This study analyzed 30 samples from Songkhla Lake (SKL) and the Lower Gulf of Thailand (LGT) to assess their genetic diversity, structure, and connectivity using 16 microsatellite loci. Extremely low genetic diversity was observed in SKL (Ho = 0.039±0.039; AR = 1.122±0.489) and LGT (Ho = 0.033±0.033; AR = 1.141±0.566) populations. Population differentiation (FST = 0.033, p>0.05) and clustering analyses based on both Principal Coordinate Analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) suggest limited genetic divergence and potential panmixia (single genetic pool) between both populations. These findings highlight critical conservation concerns due to low diversity despite the lack of isolation, emphasizing the need for immediate and targeted efforts to ensure the long-term viability of this iconic yet vulnerable population.
... Given that the primary goal of population genetics is to comprehend the factors shaping patterns of genetic diversity within and among populations, as well as to understand the drivers of genetic diversity patterns (Vachon et al., 2018), analysis mtDNA diversity in sperm whales, considering environmental changes over short periods, such as those re-cently observed in the GC, may provide insights into how sperm whales are responding to such changes. ...
... In this context, cosmopolitan marine fishes with continuous distributions exhibited far less genetic structuring than species with discontinuous distributions (Graves, 1998;Schwartz and Boness, 2017). The low level of phylogeographic structure found in Southern Hemisphere K. breviceps may indicate substantial current gene flow among populations, inhibiting genetic differentiation of local populations (Avise, 1994;Vachon et al., 2018). ...
Little is known about the biology of pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales as these animals are difficult to observe in the wild. However, both species strand frequently along the South African, Australian and New Zealand coastlines, providing samples for these otherwise inaccessible species. The use of DNA samples from tissue and DNA extracted from historical material, such as teeth and bone, allowed a first analysis of the population structure of both species in the Southern Hemisphere.
... Many cetaceans (dolphins, whales and porpoises) show high degrees of genetic structuring despite a markedly reduced molecular substitution rate and long generation times compared to other vertebrates (McGowen et al., 2012;Tollis et al., 2019;Vachon et al., 2018). ...
Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. trun-catus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that ex-tant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting data-set consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes.
Keywords: bottlenose dolphin, colonization, ddRAD, demographic modelling, Tursiops
... Further, depending on the migration pattern and rate, the number of subpopulations, and their individual N ex , time to equilibrium may be so long that in practical situations it can be assumed to never occur, highlighting the importance for considering N e dynamics during departures from equilibrium (Vachon et al. 2018).The divergent characteristics of subpopulations and metapopulations during departures from equilibrium found here were first noted by Varvio et al. (1986) but have received relatively little attention, despite implications for conservation and management (but see Lacy 1987;Mills and Allendorf 1996;Whitlock and McCauley 1999). Our study adds to the limited research aimed at describing the effects of extinction over contemporary time with conclusions that offer a wide range of practical implications for conservation and management. ...
Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.
... Detailed focus within taxonomic groups demonstrated correlations between range size and genetic diversity in Drosophila (Leffler et al. 2012), Australian lizards (Singhal et al. 2017b), and cetaceans (Vachon et al. 2018), but not in butterflies (Mackintosh et al. 2019). To our knowledge, we provide the first evidence that total range size may be a useful predictor of squamate genomic diversity. ...
Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R 2 = 0.31, p = 0.007) and GBS diversity (R 2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
