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Cross-species amplification of microsatellites in crocodilians: Assessment and applications for the future

August 2008
Conservation Genetics 10(4):935-954

DOI:10.1007/s10592-008-9601-6

Authors:

Latonia Miles

Steward Health Care System

Stacey Lyn Lance

University of Georgia

Sally R Isberg

Centre for Crocodile Research, Noonamah, Northern Territory, Australia

Chris Moran

The University of Sydney

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Microsatellite DNA loci have emerged as the dominant genetic tool for addressing questions associated with genetic diversity in many wildlife species, including crocodilians. Despite their usefulness, their isolation and development can be costly, as well as labour intensive, limiting their wider use in many crocodilian species. In this study, we investigate the cross-species amplification success of 82 existing microsatellites previously isolated for the saltwater crocodile (Crocodylus porosus) in 18 non-target crocodilian species; Alligator sinensis, Caiman crocodylus, Caiman latirostris, Caiman yacare, Melanosuchus niger, Paleosuchus palpebrosus, Crocodylus acutus, Mecistops cataphractus, Crocodylus intermedius, Crocodylus johnstoni, Crocodylus mindorensis, Crocodylus moreletii, Crocodylus niloticus, Crocodylus novaeguineae, Crocodylus palustis, Crocodylus rhombifer, Crocodylus siamensis, and Osteolaemus tetraspis. Our results show a high level of microsatellites cross-amplification making available polymorphic markers for a range of crocodilian species previously lacking informative genetic markers.

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SHORT COMMUNICATION

Cross-species ampliﬁcation of microsatellites in crocodilians:

assessment and applications for the future

Lee G. Miles ÆStacey L. Lance ÆSally R. Isberg Æ

Chris Moran ÆTravis C. Glenn

Received: 14 April 2008 / Accepted: 18 April 2008 / Published online: 8 May 2008

ÓSpringer Science+Business Media B.V. 2008

Microsatellite DNA loci have emerged as the dominant

genetic tool for addressing questions associated with genetic

diversity in many wildlife species, including crocodilians.

Despite their usefulness, their isolation and development can

be costly, as well as labour intensive, limiting their wider use

in many crocodilian species. In this study, we investigate the

cross-species ampliﬁcation success of 82 existing micro-

satellites previously isolated for the saltwater crocodile

(Crocodylus porosus) in 18 non-target crocodilian species;

Alligator sinensis,Caiman crocodylus,Caiman latirostris,

Caiman yacare,Melanosuchus niger,Paleosuchus palpe-

brosus,Crocodylus acutus,Mecistops cataphractus,

Crocodylus intermedius,Crocodylus johnstoni,Crocodylus

mindorensis,Crocodylus moreletii,Crocodylus niloticus,

Crocodylus novaeguineae,Crocodylus palustis,Crocodylus

rhombifer,Crocodylus siamensis, and Osteolaemus tetra-

spis. Our results show a high level of microsatellites cross-

ampliﬁcation making available polymorphic markers for a

range of crocodilian species previously lacking informative

genetic markers.

Keywords Crocodile Crocodilian Microsatellites 

Cross-species ampliﬁcation

Introduction

Microsatellite DNA loci (short tandem repeats) have

emerged as one of the most popular and powerful choices

of molecular markers for researchers addressing questions

of genetic diversity. They are ubiquitous in most eukaryote

genomes (Moran 1993) and provide hyper-variable

sequence tagged single locus markers capable of providing

relatively contemporary estimates of migration and relat-

edness among individuals (Selkoe and Toonen 2006; Miles

et al. unpublished data). For these reasons, microsatellites

have been widely used for population studies in a variety of

wildlife species (Wilson et al. 2004). In crocodilians,

microsatellites have been used to assess genetic diversity,

mating behaviour, hybridisation, as well as dispersal sys-

tems, in a variety of species (Glenn et al. 1996,1998;

Fitzsimmons et al. 2001; Dever et al. 2002; Davis et al.

2002; Dessauer et al. 2002; Verdade et al. 2002; Isberg

et al. 2004,2006). Despite this, informative microsatellite

markers still do not exist for many crocodilian species

(Glenn et al. 1998).

Crocodilians are an ancient lineage of reptiles comprising

nine genera and 23 species. These include alligators, caiman,

crocodiles, false crocodiles, and gharials. Crocodilians are

also the sole surviving reptilian archosaurs, a group of

diapsids that include dinosaurs and other ancient reptiles.

Despite a long and impressive history, the past century has

seen crocodilians face overwhelming threats from human

habitation. Fortunately today, many crocodilians are

recovering from the human exploitations that occurred

during the ﬁrst half of the 20th century. These exploitations

L. G. Miles (&)S. R. Isberg C. Moran

Faculty of Veterinary Science, University of Sydney, Room 513,

RMC Gunn Building, Sydney, NSW 2006, Australia

e-mail: l.miles@usyd.edu.au

S. L. Lance T. C. Glenn

Savannah River Ecology Laboratory, University of Georgia,

P.O. Drawer E, Aiken, SC 29802, USA

S. R. Isberg

Porosus Pty Ltd, PO Box 86, Palmerston, NT 0831, Australia

T. C. Glenn

Department of Environmental Health Science, University

of Georgia, Athens, GA 30602, USA

123

Conserv Genet (2009) 10:935–954

DOI 10.1007/s10592-008-9601-6

impacted crocodilian numbers and inevitably the genetic

structure and diversity within these populations (Davis et al.

2002). Although recovery programs have bolstered croco-

dilian numbers, 17 of the 23 species are still listed as CITES

Appendix I in various regions, and the pressures of illegal

hunting, habitat fragmentation and human encroachment

continue to loom for a range of vulnerable crocodilians. In

addition to previous threats, the elimination of spatial and

temporal boundaries through modern anthropogenic pres-

sures has facilitated hybridization in crocodiles by bringing

together crocodilian species that would otherwise not breed

due to a lack of opportunity (Fitzsimmons et al. 2002). This

has been identiﬁed in several Crocodylus species such as

Crocodylus rhombifer,Crocodylus moreletti,Crocodylus

siamensis and Crocodylus porosus (Ramos et al. 1994;

Fitzsimmons et al. 2002; Ray et al. 2004). Problems such as

these exemplify the need for further polymorphic markers to

assist in population studies to assess the vulnerability status

of some species. Genetic studies provide information perti-

nent to the development of management plans by identifying

conservation units for many threatened and endangered

species. However, these studies hinge on the development

and availability of genetic tools to address the contemporary

issues facing wildlife species. We aim to address this

shortfall in molecular resources for some crocodilians.

Microsatellites have been isolated for a variety of dif-

ferent species including Alligator mississipiensis (Glenn

et al. 1998), Caiman latirostris (Zucoloto et al. 2002),

Crocodylus moreletii (Dever and Densmore 2001), Croc-

odylus johnstoni and Crocodylus porosus (Fitzsimmons

et al. 2001; Miles et al. unpublished data). To date, most of

the microsatellites cited in the literature were originally

developed from either the American alligator (Alligator

mississipiensis) or the saltwater crocodile (Crocodylus

porosus), and later cross-ampliﬁed in other closely related

non-target species for wider application. Although cross-

species ampliﬁcation has been successfully employed

among closely related crocodilians (Dever et al. 2002;

Fitzsimmons et al. 2002; Zucoloto et al. 2006), most

examples have been within Alligatoridae family, with few

polymorphic markers for true Crocodylid members. Glenn

et al. (1996) noted that microsatellites isolated from the

American alligator were signiﬁcantly less likely to amplify

orthologous loci from distantly related species such as

those in the Crocodylidae family. This is not surprising

given the divergence time of alligators and crocodiles,

which is estimated to be 140 MYA (Janke et al. 2005).

Thus, a major limiting factor currently affecting the

broader application of microsatellites in crocodilian

research, especially for ‘‘true crocodiles’’, is the lack of

suitable universal primers capable of amplifying homolo-

gous loci in a large range of species. Since the isolation and

development of microsatellites is both labour intensive and

costly, we have prospected the utility of a large set of novel

microsatellites recently isolated from Crocodylus porosus

for genetic mapping purposes (Miles et al. unpublished

data), in a range of non-target crocodilians. In addition to

the cost, the reported low levels of repetitive sequence in

non-avian reptiles reported by Shedlock et al. (2007) could

potentially limit the rapid isolation and development of

microsatellites in other crocodilian species, and make the

task more expensive.

Therefore, the practical beneﬁts of cross-species

ampliﬁcation in wildlife such as birds and non-avian rep-

tiles are arguably greater than that of mammalian species.

Indeed, cross-species ampliﬁcation has proved sufﬁciently

successful in such a wide range of species (Moore et al.

1991) that evolutionary genetic studies have been con-

ducted based solely on cross-ampliﬁed microsatellites

(Primmer et al. 2005). With this in mind, we are optimistic

that the evaluation of these Crocodylus porosus microsat-

ellites will generate multiple markers useful for future

research in a variety of crocodilians currently lacking

informative genetic resources. In this communication, we

present an assessment of the microsatellite cross-species

ampliﬁcation, as well as speculate on their future value to

crocodilian researchers.

Methods

Two hundred and ﬁfty three novel microsatellites were

developed by Miles et al. (unpublished data) for the

purpose of constructing the ﬁrst crocodilian (Crocodylus

porosus) genetic-linkage map. From the framework map,

82 microsatellites were selected for whole genome scans

based on their relatively even map distribution and high

polymorphic content in the Crocodylus porosus mapping

resource. Fortuitously, these criteria are highly desirable

for genetic markers employed in population and evolu-

tionary genetic studies, and thus the suite of 82

microsatellites was retained for cross-species ampliﬁcation.

The markers chosen were those displaying the highest

levels of polymorphism in Crocodylus porosus, as it has

been commonly observed that a negative relationship exists

between cross-species ampliﬁcation/polymorphism success

and the evolutionary distance from the source species

(Glenn et al. 1996; Primmer et al. 2005). This was pref-

erable in order to retain high polymorphic content for

microsatellites in the respective crocodilian species.

The species included in this scan were the Chinese alligator

(Alligator sinensis), spectacled caiman (Caiman crocodylus),

broad-snouted caiman (Caiman latirostris), Jacare

´caiman

(Caiman yacare), black caiman (Melanosuchus niger),

Cuvier’s dwarf caiman (Paleosuchus palpebrosus), American

crocodile (Crocodylus acutus), slender-snouted crocodile

936 Conserv Genet (2009) 10:935–954

123

Table 1 Summary of locus ampliﬁcation success in Crocodilians

Locus Crocodylus

Crocodilidae Alligatoridae

C.ac C.pal C.sia C.mor M.cat C.nil O.tet C.min C.rho C.nov C.jo C.int C.cro C.lat M.nig P.pal C.ya A.sin

CpDi06 ++ + + + + + + + + ++ + + + + ++

CpDi10 ++ + + + + + + + + ++ + - - + -+

CpDi11 ++ + + + + + + + + ++ - - - - --

CpDi13 ++ + + + + + + + - ++ ± + + + ±+

CpDi21 +- + + + + - + ± - -+ - - - - --

CpDi24 ++ + + + + ± + + + ++ + + + + ++

CpDi28 ++ + + + + ± + + + ++ + - - - --

CpDi29 ++ + + + + ± + + + ++ + + + ± ++

CpDi41 ++ + + + + ± + + + ++ + + + + ±-

CpDi42 ++ + + + + ± + + + ++ - - - - ++

CpF509 ++ + + + + ± + + + ++ + + - + -+

CpP106 ++ + + + + ± + + + ++ ± - - - --

CpP114 ++ + + + + ± + + + ++ - - - - --

CpP116 ++ + + + + ± + + + ++ ± ± - + -+

CpP121 ++ + + + + ± + + + ++ - - - + -±

CpP205 ++ + + + + ± + + + ++ ± - - - --

CpP218 ++ + + + + ± + + + -+ + + + + +±

CpP302 ++ + + + + ± + + + ++ - - - - --

CpP305 ++ + + + + ± + + + ++ - - + - +-

CpP307 ++ + + + + ± - ± - ++ + ± + - --

CpP309 ++ + + + + ± + + + ++ - - + + --

CpP314 ++ + + + + ± + + + ++ + + ± + ±+

CpP405 ++ + + + + ± + + + ++ + + + ± ++

CpP610 ++ + + + + - + + + ++ + + + + ++

CpP706 ++ + + + + ± + + + ++ + ± ± + ++

CpP722 ++ + + + + - + + + ++ + - ± - --

CpP801 ++ + + + + - + + + ++ - - - - -+

CpP803 +- + - + - - + ± - -+ - - - - --

CpP815 ++ + + + + - + + + ++ - - - - --

CpP903 ++ + + + + + + + + ++ + + - + ++

CpP906 ++ - ± + + - - + + -+ - - - - --

CpP914 ++ + + + + + + + + ++ + + + + ++

CpP1303 ++ + + + + + + + + ++ - - - - --

Conserv Genet (2009) 10:935–954 937

123

Table 1 continued

Locus Crocodylus

Crocodilidae Alligatoridae

C.ac C.pal C.sia C.mor M.cat C.nil O.tet C.min C.rho C.nov C.jo C.int C.cro C.lat M.nig P.pal C.ya A.sin

CpP1401 ++ ++ + +++ + + +++ ++ +++

CpP1404 ++ ++ + +++ - + ++± -- ---

CpP1409 ++ ++ + +-+ + + ++- -- ---

CpP1416 ++ ++ + +++ + + ++- -- ---

CpP1603 ++ ++ + +++ + + ++± -- ---

CpP1610 +- ++ + +++ + + +++ ++ -+-

CpP1708 ++ ++ + +++ + + +++ ++ +++

CpP2201 +- ++ + +++ + + ++± -- ±--

CpP2206 ++ ++ + +++ + + +++ ±+ +±±

CpP2504 ++ ++ - +-+ + + ++- -- ±--

CpP2514 ++ ++ + +++ + + ++- -- ---

CpP2516 ++ ++ + +++ + + +++ +± +±+

CpP2704 ++ ++ + +++ + + ++± -- --±

CpP2706 ++ ++ + +++ + + ++- +- ±-+

CpP2815 ++ ++ + +++ + + +++ -± ±±+

CpP2902 -- ++ + +++ + + ±±+ ±+ -++

CpP3004 ++ ++ + +++ + + +++ -- ---

CpP3211 ++ ++ + +++ + + ++- -- ---

CpP3215 -- -- - --- - - --+ -- ---

CpP3216 ++ ++ + +++ + + ++± +- ---

CpP3217 -- -- - --- - - --- -- ---

CpP3220 ++ ++ + +++ + + +++ ±± ±--

CpP3303 ++ ++ + +++ + + ++- ++ +-+

CpP3309 ++ ++ + +++ + + +++ ++ +++

CpP3313 ++ ++ + +++ + + +++ -- ---

CpP3314 ++ ++ + +++ + + +++ ++ +++

CpP3601 ++ ++ + +++ + + ++- -- ±-+

CpP3603 ++ ++ + +++ + - ++- -- ---

CpP4004 ++ ++ + +++ + + +++ +± ±--

CpP4006 ++ ++ + +++ + + ++± -- ±--

CpP4010 ++ ++ + +++ + + ++± -- ---

CpP4013 ++ ++ + +++ + + +++ ++ -++

CpP4116 ++ ++ + +±+ + + ++- -- ---

938 Conserv Genet (2009) 10:935–954

123

(Mecistops cataphractus), Orinoco crocodile (Crocodylus

intermedius), Australian freshwater crocodile (Crocodylus

johnstoni), Philippine crocodile (Crocodylus mindorensis),

Morelet’s crocodile (Crocodylus moreletii), Nile crocodile

(Crocodylus niloticus), New Guinea Crocodile (Crocodylus

novaeguineae), mugger (Crocodylus palustis), Cuban croco-

dile (Crocodylus rhombifer), Siamese crocodile (Crocodylus

siamensis) and African dwarf crocodile (Osteolaemus tetra-

spis). Species and sample numbers are provided in Tables 1–3.

The microsatellites were ampliﬁed according to the

respective conditions previously described for Crocodylus

porosus (Miles et al. unpublished data). No further opti-

misation of these primers was attempted, so it is likely that

some primers here could be further optimized for various

crocodilian species.

The limited number of samples that were available for

many of the species included in this investigation compli-

cated the generation of allele frequency statistics.

Although, CERVUS version 3.0 (Kalinowski et al. 2007)

was used to efﬁciently estimate the number of alleles per

locus (k), statistics such as observed heterozygosity (H

obs

)

and Polymorphic Information Content (PIC) for each locus

were not generated due to low sample number.

Results and discussion

We attempted to amplify 82 microsatellite loci in 70

individuals across 18 species of crocodilians. The intention

of this scan was not to exhaustively evaluate each micro-

satellite for each and every crocodilian, but to present

strong evidence for speciﬁc microsatellite cross-ampliﬁ-

cation, and provide preliminary information pertaining to

the utility of the microsatellites where possible. The suc-

cess of locus ampliﬁcations for the crocodilians included in

this study are summarised in Table 1. Allele numbers and

ranges, along with the DNA sample numbers are presented

in Table 2for Crocodilidae species, and in Table 3for

Alligatoridae species.

The success of heterologous microsatellite ampliﬁcation

observed in this study ranged widely with an average

ampliﬁcation success of 90% among Crocodilidae species

(ranging from 56% to 96%), an average of 35% ampliﬁ-

cation success among Caiman species (ranging from 27%

to 47%) and 41% ampliﬁcation success for the Chinese

Alligator (Alligator sinensis). To be more conservative,

these values were calculated with consideration for

ambiguous ampliﬁcations, which to avoid over estimating

success rates, was taken to be negative. It was evident that

the success of cross-ampliﬁcation was highly correlated

with the evolutionary distance of the crocodilian of interest

to the microsatellite source species, with the highest levels

of ampliﬁcation observed in Crocodylid species. These

Table 1 continued

Locus Crocodylus

Crocodilidae Alligatoridae

C.ac C.pal C.sia C.mor M.cat C.nil O.tet C.min C.rho C.nov C.jo C.int C.cro C.lat M.nig P.pal C.ya A.sin

CpP4208 +- + + + + + + - - +- - - - - --

CpP4301 ++ + + + + + + + + ++ + + + ± -+

CpP4304 ++ + + + + + + + + ++ - - - - --

CpP4308 ++ + + + + + + + + ++ + - ± - ±+

CpP4311 ++ + + + + + + + + ++ + + + - ++

Species key: C.ac, Crocodylus acutus; C.pal, Crocodylus palustris; C.sia, Crocodylus siamensis; C.mor, Crocodylus moreletii; M.cat, Mecistops cataphractus; C.nil, Crocodylus niloticus; O.tet,

Osteolaemus tetraspis; C.min, Crocodylus mindorensis; C.rho, Crocodylus rhombifer; C.nov, Crocodylus novaeguineae; C.jo, Crocodylus johnstoni; C.int, Crocodylus intermedius; C.cro,

Caiman crocodylus; C.lat, Caiman latirostris; M.nig, Melanosuchus niger; P.pal, Paleosuchus palpebrosus; C.ya, Caiman yacare; A.sin, Alligator sinensis

Score key: +, Good ampliﬁcation; -, No ampliﬁcation; ±Ambiguous

Conserv Genet (2009) 10:935–954 939

123

Table 2 Microsatellite locus information, including sample size (N), observed number of alleles (K) and allele ranges for Crocodildae spp.

Locus accession Repeat motif Crocodilidae

C. acutus C. palustrus C. siamensis C. moreletti M. cataphractus C .niloticus

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpDi06

EU593279

(AC)

236–274 6 8 245 1 1 234–259 5 8 239 1 3 241–255 6 8 236-274 8 8

CpDi10

EU593283

(AC)

(CT)

251–253 2 8 247 1 1 251–261 4 8 251–253 2 3 247–255 3 8 249–255 2 8

CpDi11

EU593284

(AC)

172 1 8 174 1 1 173–190 6 8 174 1 3 183–187 3 8 178–184 4 8

CpDi13

EU593286

(AC)

361–374 3 8 359 1 1 320–386 7 8 347–363 2 3 347–374 3 8 364–374 5 8

CpDi21

EU593290

(AC)

171–178 2 8 N/A – 1 169–174 2 8 166–169 2 3 163–182 5 8 163–190 6 8

CpDi24

EU593293

(AC)

134–136 2 8 142 1 1 120–169 4 8 152–155 2 3 120–150 5 8 136–155 8 8

CpDi28

EU593295

(AC)

131–137 4 8 120 1 1 120–131 4 8 131–135 2 3 126–129 3 8 118–152 5 8

CpDi29

EU593296

(AC)

247–249 2 8 254–256 2 1 243–249 4 8 241–252 2 3 234–262 5 8 249–164 6 8

CpDi41

EU593301

(AC)

187 1 8 183 1 1 185–189 2 8 187 1 3 185–189 2 8 187–189 2 8

CpDi42

EU593302

(AC)

115–138 4 8 133 1 1 135–168 7 8 122–133 2 3 101–102 2 8 117–138 8 8

CpF509

EU593315

(AC)

324–328 3 8 317 1 1 312–335 5 8 307–312 3 3 317–356 7 8 313–324 5 8

CpP106

EU593323

(ATAG)

252–260 3 8 240 1 1 240–244 2 8 264–268 2 3 231 1 8 256–260 2 8

CpP114

EU593329

(AGAT)

189 1 8 189 1 1 181–185 2 8 189–194 2 3 200–213 2 8 187–201 2 8

CpP116

EU593331

(AGAT)

267–273 3 8 269 1 1 269 1 8 273–282 2 3 257–262 2 8 269–278 2 8

CpP121

EU593333

(AGAT)

163–171 2 8 159 1 1 171–187 5 8 163–175 3 3 163–183 5 8 151–159 2 8

CpP205

EU593338

(AGAT)

329 1 8 334 1 1 325–345 4 8 329 1 3 321–349 4 8 325–338 3 8

940 Conserv Genet (2009) 10:935–954

123

Table 2 continued

Locus accession Repeat motif Crocodilidae

C. acutus C. palustrus C. siamensis C. moreletti M. cataphractus C .niloticus

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP218

EU593346

(ACCC)

181–185 2 8 170 1 1 170 1 8 185–193 3 3 172 1 8 170–197 7 8

CpP302

EU593350

(AC)

193–211 5 8 191 1 1 191–196 5 8 203–216 3 3 165–173 3 8 173–224 9 8

CpP305

EU593352

(AC)

204–213 4 8 192 1 1 186–221 9 8 196–229 3 3 188–234 6 8 180–242 13 8

CpP307

EU593353

(ACTC)

342–373 5 8 319 1 1 382–416 4 8 370–392 2 3 315–331 4 8 310–378 8 8

CpP309

EU593354

(AAAC)

214–231 4 8 212 1 1 207–222 3 8 214–219 2 3 226–228 2 8 224–294 8 8

CpP314

EU593357

(AGAT)

261–267 3 8 248 1 1 225–263 4 8 260–278 4 3 235–275 4 8 248–275 6 8

CpP405

EU593361

(AAAG)

191 1 8 191 1 1 191–195 2 8 191 1 3 179 1 8 187–195 3 8

CpP610

EU593371

(ACAG)

225–250 4 8 242–256 2 1 254 1 8 227 1 3 231–233 2 8 227–228 2 8

CpP706

EU593375

(ACAG)

86–93 2 8 86 1 1 86 1 8 86 1 3 89–101 3 8 86–101 2 8

CpP722

EU593381

(ACAG)

(AG)

147–182 4 8 131 1 1 133–138 5 8 139 1 3 N/A 0 8 123–198 4 8

CpP801

EU593382

(AGAT)

164–176 4 8 156–160 2 1 137–153 3 8 179–192 3 3 N/A 0 8 160–188 7 8

CpP804

EU593383

(AGAT)

190–198 3 8 N/A – 1 177 1 8 N/A – 3 N/A 0 8 N/A – 8

CpP815

EU593390

(AGAT)

230 1 8 239 1 1 236–257 5 8 235–239 2 3 N/A 0 8 233–243 3 8

CpP903

EU593391

(ACT)

230 1 8 226 1 1 226 1 8 230 1 3 217–226 2 8 226–230 2 8

CpP906

EU593392

(ACAG)

281–325 2 8 322 1 1 N/A – 8 293 1 3 N/A 0 8 281–316 2 8

CpP914

EU593395

(AGAT)

255–263 2 8 279 1 1 267–275 2 8 267–275 2 3 215–267 5 8 255–267 4 8

Conserv Genet (2009) 10:935–954 941

123

Table 2 continued

Locus accession Repeat motif Crocodilidae

C. acutus C. palustrus C. siamensis C. moreletti M. cataphractus C .niloticus

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP1303

EU593414

(AAAC)

235 1 8 235 1 1 235 1 8 235 1 3 235–243 2 8 235 1 8

CpP1401

EU593419

(AGAT)

170 1 8 174 1 1 170–178 2 8 170 1 3 174–191 5 8 170 1 8

CpP1404

EU593421

(AGAT)

294–307 3 8 311–322 2 1 268–290 6 8 277 1 3 264–284 4 8 179–311 4 8

CpP1409

EU593425

(AGAT)

235–264 2 8 259–267 2 1 236–264 7 8 271–289 2 3 255–277 3 8 251–279 9 8

CpP1416

EU593429

(ACAT)

186–192 2 8 203–205 2 1 203–209 6 8 200 1 3 190–199 2 8 179–192 4 8

CpP1603

EU593433

(AGAT)

304–312 2 8 308 1 1 312 1 8 312 1 3 310 1 8 307–320 4 8

CpP1610

EU593437

(AGAT)

300–304 2 8 N/A – 1 288–296 2 8 296–304 3 3 288–304 4 8 299–307 5 8

CpP2201

EU593442

(ACAG)

224 1 8 N/A – 1 224–240 5 8 220 1 3 214–216 2 8 220–226 4 8

CpP2206

EU593445

(AAAG)

235 1 8 243 1 1 239–243 2 8 235 1 3 239–262 4 8 235–243 3 8

CpP2504

EU593451

(AGAT)

332–379 4 8 342 2 1 319–366 6 8 308 1 3 N/A 0 8 327–368 8 8

CpP2514

EU593456

(AGAT)

181 1 8 158 1 1 171 1 8 172 1 3 181–196 4 8 171–175 3 8

CpP2516

EU593457

(AAC)

290–293 2 8 290 1 1 296–299 2 8 293–306 3 3 291–294 2 8 290–296 3 8

CpP2704

EU593458

(AGAT)

140 1 8 148 1 1 140–145 2 8 135 1 3 140–145 2 8 140 1 8

CpP2706

EU593460

(AAAC)

330 1 8 330 1 1 334 1 8 330 1 3 332 1 8 330–338 3 8

CpP2815

EU593465

(ATC)

164 1 8 163 1 1 163 1 8 163 1 3 157 1 8 154–163 2 8

CpP2902

EU593468

(ATC)

N/A – 8 N/A – 1 386 1 8 380–389 2 3 377 1 8 380–395 3 8

942 Conserv Genet (2009) 10:935–954

123

Table 2 continued

Locus accession Repeat motif Crocodilidae

C. acutus C. palustrus C. siamensis C. moreletti M. cataphractus C .niloticus

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP3004

EU593474

(AGAT)

(ACCT)

126–130 2 8 146 1 1 130–138 2 8 146–162 2 3 126–166 6 8 126–154 6 8

CpP3211

EU593479

(AAAC)

314 1 8 323 1 1 321 1 8 314 1 3 310 1 8 310–315 3 8

CpP3215

EU593482

(AGAT)

N/A – 8 N/A – 1 N/A – 8 N/A – 3 N/A 0 8 N/A – 8

CpP3216

EU593483

(ACAG)

140 1 8 140 1 1 140 1 8 140 1 3 140 1 8 140 1 8

CpP3217

EU593484

(AAAC)

N/A – 8 N/A – 1 N/A – 8 N/A – 3 N/A 0 8 N/A – 8

CpP3220

EU593486

(AAAC)

117 1 8 127 1 1 123 1 8 117 1 3 123 1 8 117 1 8

CpP3303

EU593488

(AACC)

363 1 8 363 1 1 355–375 2 8 375 1 3 363 1 8 367–383 5 8

CpP3309

EU593490

(AGAT)

160–164 2 8 189 1 1 164 1 8 160 1 3 172–193 3 8 153–172 4 8

CpP3313

EU593491

(AGAT)

365 1 8 365 1 1 369–385 3 8 390–402 2 3 369–385 4 8 365–374 3 8

CpP3314

EU593492

(AGAT)

312–324 3 8 312 1 1 300–304 2 8 308–332 4 3 300–304 2 8 304–308 2 8

CpP3601

EU593503

(AAC)

162–167 3 8 165 1 1 167–173 3 8 161 1 3 162–164 2 8 161–167 3 8

CpP3603

EU593504

(AGAT)

376–380 2 8 364 1 1 376–392 3 8 376–380 2 3 359 1 8 368–372 2 8

CpP4004

EU593510

(AGAT)

395–419 5 8 407 1 1 400–416 3 8 399–403 2 3 374–390 4 8 382–403 4 8

CpP4006

EU593511

(AGAT)

95–103 3 8 103 1 1 99–103 2 8 103–107 2 3 95 1 8 91–120 6 8

CpP4010

EU593513

(ACAT)

200–209 4 8 206 1 1 200 1 8 210 1 3 196–200 2 8 202–206 3 8

CpP4013

EU593514

(AAAG)

360–361 2 8 361 1 1 361 1 8 361–362 2 3 361–372 3 8 361–364 3 8

Conserv Genet (2009) 10:935–954 943

123

Table 2 continued

Locus accession Repeat motif Crocodilidae

C. acutus C. palustrus C. siamensis C. moreletti M. cataphractus C .niloticus

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP4116

EU593518

(AGAT)

209–226 4 8 218–226 2 1 214–230 2 8 214–226 3 3 199–205 3 8 205–222 4 8

CpP4208

EU593520

(AGAT)

N/A – 8 N/A – 1 160 1 8 160 1 3 188–228 6 8 N/A – 8

CpP4301

EU593522

(ACT)

352–355 2 8 340 1 1 355–382 6 8 355–358 2 3 340 1 8 340 1 8

CpP4304

EU593524

(AAC)

125 1 8 131 1 1 119 1 8 134 1 3 122–134 2 8 125–137 3 8

cpP4308

EU593525

(ATC)

105–120 3 8 102 1 1 102–111 3 8 117 1 3 98 1 8 108–127 6 8

CpP4311

EU593526

(AGAT)

198–227 5 8 211–215 2 1 207–215 3 8 198 1 3 203–207 2 8 203–239 9 8

Locus accession Repeat motif O. tetraspis C. mindorensis C. rhombifer C. novaguineae C. johnsoni C. intermedius

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpDi06

EU593279

(AC)

230–236 2 8 261–266 2 1 226–245 2 3 255 1 1 247 1 2 288–293 2 2

CpDi10

EU593283

(AC)

(CT)

253–268 6 8 257 1 1 251 1 3 253 1 1 247 1 2 259 1 2

CpDi11

EU593284

(AC)

172–203 7 8 183 1 1 172 1 3 174 1 1 184 1 2 172 1 2

CpDi13

EU593286

(AC)

342–374 4 8 361–363 2 1 363–372 2 3 N/A – 1 359 1 2 361–374 2 2

CpDi21

EU593290

(AC)

163–174 2 8 180–184 2 1 169–171 2 3 N/A – 1 N/A – 2 169 1 2

CpDi24

EU593293

(AC)

101–145 6 8 142 1 1 146–148 2 3 146–152 2 1 144 1 2 152 1 2

CpDi28

EU593295

(AC)

109–131 4 8 126 1 1 120–135 2 3 141–143 2 1 126 1 2 141–145 2 2

CpDi29

EU593296

(AC)

244–246 2 8 249 1 1 247 1 3 269–270 2 1 247 1 2 243 1 2

CpDi41

EU593301

(AC)

189–195 2 8 187 1 1 187 1 3 185 1 1 185 1 2 187 1 2

944 Conserv Genet (2009) 10:935–954

123

Table 2 continued

Locus accession Repeat motif O. tetraspis C. mindorensis C. rhombifer C. novaguineae C. johnsoni C. intermedius

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpDi42

EU593302

(AC)

96–117 4 8 126 1 1 113 1 3 115 1 1 107 1 2 111 1 2

CpF509

EU593315

(AC)

301 1 8 320 1 1 320 1 3 324 1 1 307 1 2 313 1 2

CpP106

EU593323

(ATAG)

244–247 2 8 247–256 2 1 244 1 3 244 1 1 247 1 2 244 1 2

CpP114

EU593329

(AGAT)

194–198 3 8 181 1 1 194–195 2 3 189 1 1 201 1 2 209–211 2 2

CpP116

EU593331

(AGAT)

259–280 3 8 261 1 1 273 1 3 261 1 1 273 1 2 269 1 2

CpP121

EU593333

(AGAT)

159–173 5 8 163 1 1 159 1 3 171 1 1 171 1 2 163 1 2

CpP205

EU593338

(AGAT)

321–349 6 8 317 1 1 317 1 3 317 1 1 309 1 2 325 1 2

CpP218

EU593346

(ACCC)

172 1 8 173 1 1 177–181 2 3 185 1 1 N/A – 2 201–205 2 2

CpP302

EU593350

(AC)

183–205 7 8 187 1 1 209–220 3 3 181 1 1 203–207 3 2 199–218 3 2

CpP305

EU593352

(AC)

165 1 8 199–201 2 1 233 1 3 176 1 1 188–197 2 2 194–197 3 2

CpP307

EU593353

(ACTC)

312–315 2 8 N/A – 1 333 1 3 N/A – 1 322 1 2 333–342 2 2

CpP309

EU593354

(AAAC)

226 1 8 219 1 1 214–224 2 3 214–219 2 1 209 1 2 219 1 2

CpP314

EU593357

(AGAT)

240–242 2 8 257 1 1 246 1 3 263–265 2 1 232 1 2 255–263 3 2

CpP405

EU593361

(AAAG)

179 1 8 195 1 1 191 1 3 195 1 1 191 1 2 191 1 2

CpP610

EU593371

(ACAG)

225–259 5 8 268 1 1 242–264 2 3 256 1 1 254 1 2 227 1 2

CpP706

EU593375

(ACAG)

86 1 8 86–89 2 1 86 1 3 86 1 1 86–89 2 2 86–93 2 2

CpP722

EU593381

(ACAG)

(AG)

127–129 2 8 131 1 1 149–161 2 3 127–135 2 1 141 1 2 145 1 2

Conserv Genet (2009) 10:935–954 945

123

Table 2 continued

Locus accession Repeat motif O. tetraspis C. mindorensis C. rhombifer C. novaguineae C. johnsoni C. intermedius

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP801

EU593382

(AGAT)

N/A – 8 160–180 2 1 164–176 2 3 160 1 1 176–192 2 2 180–188 3 2

CpP804

EU593383

(AGAT)

N/A – 8 177 1 1 194 1 3 N/A – 1 N/A – 2 190 1 2

CpP815

EU593390

(AGAT)

N/A – 8 235 1 1 235–242 2 3 235 1 1 242 1 2 226–235 2 2

CpP903

EU593391

(ACT)

226 1 8 226 1 1 230 1 3 226 1 1 226 1 2 230 1 2

CpP906

EU593392

(ACAG)

N/A – 8 N/A 0 1 281 1 3 322 1 1 N/A – 2 281 1 2

CpP914

EU593395

(AGAT)

267–287 6 8 259 1 1 255 1 3 270 1 1 270 1 2 255 1 2

CpP1303

EU593414

(AAAC)

243 1 8 235 1 1 235 1 3 235 1 1 235 1 2 235 1 2

CpP1401

EU593419

(AGAT)

166–191 6 8 170 1 1 170 1 3 178–182 2 1 170 1 2 170 – 2

CpP1404

EU593421

(AGAT)

268–296 5 8 298 1 1 N/A – 3 N/A – 1 288 1 2 284 1 2

CpP1409

EU593425

(AGAT)

226–259 3 8 264 1 1 253–264 2 3 261 1 1 226 1 2 247–253 3 2

CpP1416

EU593429

(ACAT)

186–190 2 8 196 1 1 186 1 3 188 1 1 200 1 2 192 1 2

CpP1603

EU593433

(AGAT)

302–323 3 8 320 1 1 315 1 3 312–315 2 1 315 1 2 312 1 2

CpP1610

EU593437

(AGAT)

300–312 5 8 296–304 2 1 304 1 3 300 1 1 288 1 2 296–310 2 2

CpP2201

EU593442

(ACAG)

218–228 5 8 220 1 1 220–222 2 3 224 1 1 224 1 2 220 1 2

CpP2206

EU593445

(AAAG)

235–248 3 8 235 1 1 239 1 3 235 1 1 243 1 2 239 1 2

CpP2504

EU593451

(AGAT)

N/A – 8 352 1 1 351–375 3 3 351–360 2 1 349 1 2 347–351 2 2

CpP2514

EU593456

(AGAT)

187–203 6 8 184 1 1 172 1 3 184 1 1 183 1 2 178 1 2

946 Conserv Genet (2009) 10:935–954

123

Table 2 continued

Locus accession Repeat motif O. tetraspis C. mindorensis C. rhombifer C. novaguineae C. johnsoni C. intermedius

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP2516

EU593457

(AAC)

287–299 5 8 287 1 1 293–299 2 3 287 1 1 285–291 2 2 293 1 2

CpP2704

EU593458

(AGAT)

140–145 2 8 140 1 1 140 1 3 140 1 1 145 1 2 145 1 2

CpP2706

EU593460

(AAAC)

324–332 2 8 334 1 1 330 1 3 334 1 1 330 1 2 330 1 2

CpP2815

EU593465

(ATC)

157–159 2 8 167 1 1 163 1 3 167 1 1 161 1 2 163 1 2

CpP2902

EU593468

(ATC)

377 1 8 386 1 1 380 1 3 389 1 1 386 1 2 386 1 2

CpP3004

EU593474

(AGAT)

(ACCT)

109–146 4 8 142 1 1 130 1 3 122–126 2 1 122 1 2 122 1 2

CpP3211

EU593479

(AAAC)

310–311 2 8 314 1 1 314 1 3 314 1 1 315 1 2 314 1 2

CpP3215

EU593482

(AGAT)

N/A – 8 N/A 0 1 N/A – 3 N/A – 1 N/A – 2 N/A – 2

CpP3216

EU593483

(ACAG)

140 1 8 140 1 1 140 1 3 140 1 1 140 1 2 140–185 4 2

CpP3217

EU593484

(AAAC)

N/A – 8 N/A 0 1 N/A – 3 N/A – 1 N/A – 2 N/A – 2

CpP3220

EU593486

(AAAC)

125–129 2 8 136 1 1 117 1 3 131 1 1 140 1 2 117 1 2

CpP3303

EU593488

(AACC)

379–394 4 8 363 1 1 355–363 2 3 371 1 1 379 1 2 367 1 2

CpP3309

EU593490

(AGAT)

148–189 6 8 168 1 1 160 1 3 168 1 1 164 1 2 164 1 2

CpP3313

EU593491

(AGAT)

385–397 4 8 374 1 1 365–369 2 3 365 1 1 365 1 2 374–381 2 2

CpP3314

EU593492

(AGAT)

288–297 2 8 300 1 1 321–324 2 3 312 1 1 316 1 2 304 1 2

CpP3601

EU593503

(AAC)

154–162 4 8 155–162 2 1 143–160 3 3 162 1 1 158 1 2 160 1 2

CpP3603

EU593504

(AGAT)

364–380 3 8 372 1 1 368 1 3 N/A – 1 368 1 2 376 1 2

Conserv Genet (2009) 10:935–954 947

123

Table 2 continued

Locus accession Repeat motif O. tetraspis C. mindorensis C. rhombifer C. novaguineae C. johnsoni C. intermedius

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP4004

EU593510

(AGAT)

391–427 8 8 399–407 2 1 403 1 3 399 1 1 395 1 2 411 1 2

CpP4006

EU593511

(AGAT)

111–124 4 8 95 1 1 87 1 3 95 1 1 103 1 2 103 1 2

CpP4010

EU593513

(ACAT)

200–204 2 8 209 1 1 204 1 3 209–212 2 1 196 1 2 196 1 2

CpP4013

EU593514

(AAAG)

355 1 8 361 1 1 361 1 3 364 1 1 364 1 2 361 1 2

CpP4116

EU593518

(AGAT)

203–209 2 8 214 1 1 222 2 3 205–209 2 1 218–222 2 2 209 1 2

CpP4208

EU593520

(AGAT)

208–233 8 8 168 1 1 N/A – 3 N/A – 1 168 1 2 N/A – 2

CpP4301

EU593522

(ACT)

337–349 2 8 349 1 1 355–364 3 3 355 1 1 352–361 2 2 355 1 2

CpP4304

EU593524

(AAC)

122–134 4 8 125 1 1 128–134 2 3 128 1 1 119 1 2 125 1 2

cpP4308

EU593525

(ATC)

114–124 4 8 130 1 1 114–120 2 3 98–117 2 1 108 1 2 124–130 2 2

CpP4311

EU593526

(AGAT)

203–247 8 8 203 1 1 207–219 3 3 198 1 1 219–223 2 2 198–203 2 2

948 Conserv Genet (2009) 10:935–954

123

Table 3 Microsatellite locus information, including sample size (N), observed number of alleles (K) and allele ranges for Alligatoridae spp.

Locus accession Repeat motif C .crocodylus C. latirostris M. niger P. palpebrosus C. yacare A. sinensis

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpDi06

EU593279

(AC)

222 1 3 226 1 2 222 1 3 222 1 2 222 1 4 222 1 3

CpDi10

EU593283

(AC)

(CT)

247–255 2 3 N/A – 2 N/A – 3 249 1 2 N/A – 4 251–278 2 3

CpDi11

EU593284

(AC)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpDi13

EU593286

(AC)

370 1 3 370 1 2 370–374 2 3 370 1 2 374 1 4 363–374 2 3

CpDi21

EU593290

(AC)

171 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpDi24

EU593293

(AC)

111 1 3 111 1 2 113 1 3 111 1 2 111 1 4 111–190 3 3

CpDi28

EU593295

(AC)

126–128 2 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpDi29

EU593296

(AC)

246 1 3 246 1 2 246 1 3 243 1 2 246 1 4 239–246 2 3

CpDi41

EU593301

(AC)

179 1 3 185 1 2 177–185 2 3 187 1 2 182 1 4 N/A – 3

CpDi42

EU593302

(AC)

N/A – 3 N/A – 2 186 1 3 N/A – 2 95–136 2 4 87–98 2 3

CpF509

EU593315

(AC)

313–315 2 3 317 1 2 N/A – 3 319 1 2 N/A – 4 312 1 3

CpP106

EU593323

(ATAG)

244 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP114

EU593329

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP116

EU593331

(AGAT)

254 1 3 266 1 2 N/A – 3 262 1 2 N/A – 4 261–271 2 3

CpP121

EU593333

(AGAT)

N/A – 3 N/A – 2 N/A – 3 183 1 2 N/A – 4 171 1 3

CpP205

EU593338

(AGAT)

317 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP218

EU593346

(ACCC)

168 1 3 168 1 2 168 1 3 172 1 2 168 1 4 168 1 3

Conserv Genet (2009) 10:935–954 949

123

Table 3 continued

Locus accession Repeat motif C .crocodylus C. latirostris M. niger P. palpebrosus C. yacare A. sinensis

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP302

EU593350

(AC)

N/A – 3 N/A – 2 204 1 3 N/A – 2 N/A – 4 N/A – 3

CpP305

EU593352

(AC)

N/A – 3 N/A – 2 178 1 3 N/A – 2 176 1 4 N/A – 3

CpP307

EU593353

(ACTC)

331 1 3 310–333 2 2 318–344 2 3 N/A – 2 N/A – 4 N/A – 3

CpP309

EU593354

(AAAC)

260 1 3 N/A – 2 221 1 3 213–221 2 2 N/A – 4 N/A – 3

CpP314

EU593357

(AGAT)

223–255 6 3 232–242 4 2 223 1 3 228 1 2 295 1 4 229–295 2 3

CpP405

EU593361

(AAAG)

188 1 3 184 1 2 184 1 3 N/A – 2 184 1 4 188–204 2 3

CpP610

EU593371

(ACAG)

220 1 3 225 1 2 225 1 3 231 1 2 220 1 4 220–225 2 3

CpP706

EU593375

(ACAG)

86–101 2 3 N/A – 2 N/A – 3 86 1 2 86 1 4 86 1 3

CpP722

EU593381

(ACAG)

(AG)

135–234 3 3 N/A – 2 219 1 3 N/A – 2 N/A – 4 N/A – 3

CpP801

EU593382

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 132 1 3

CpP804

EU593383

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP815

EU593390

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP903

EU593391

(ACT)

226–231 4 3 230–233 2 2 N/A – 3 225 1 2 225–270 3 4 226–231 3 3

CpP906

EU593392

(ACAG)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP914

EU593395

(AGAT)

246–249 2 3 249 1 2 251 1 3 246–253 3 2 246–251 3 4 242–249 2 3

CpP1303

EU593414

(AAAC)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP1401

EU593419

(AGAT)

155–163 2 3 155–163 2 2 155 1 3 155–160 2 2 155–163 2 4 155–163 5 3

950 Conserv Genet (2009) 10:935–954

123

Table 3 continued

Locus accession Repeat motif C .crocodylus C. latirostris M. niger P. palpebrosus C. yacare A. sinensis

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP1404

EU593421

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP1409

EU593425

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP1416

EU593429

(ACAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP1603

EU593433

(AGAT)

316–320 2 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP1610

EU593437

(AGAT)

304–319 2 3 315–319 2 2 299–319 3 3 N/A – 2 319–327 3 4 N/A – 3

CpP2201

EU593442

(ACAG)

220 1 3 N/A – 2 N/A – 3 230 1 2 N/A – 4 N/A – 3

CpP2206

EU593445

(AAAG)

239–248 2 3 235 1 2 224–235 2 3 230–243 2 2 235 1 4 224 1 3

CpP2504

EU593451

(AGAT)

N/A – 3 N/A – 2 N/A – 3 349 1 2 N/A – 4 N/A – 3

CpP2514

EU593456

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP2516

EU593457

(AAC)

284–287 2 3 286–296 3 2 289–291 2 3 280–298 3 2 293 1 4 282 1 3

CpP2704

EU593458

(AGAT)

140–145 2 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 140 1 3

CpP2706

EU593460

(AAAC)

N/A – 3 316 1 2 N/A – 3 328 1 2 N/A – 4 305–326 3 3

CpP2815

EU593465

(ATC)

157–166 3 3 N/A – 2 161 1 3 161 1 2 158 1 4 153–154 2 3

CpP2902

EU593468

(ATC)

386 1 3 386 1 2 386 1 3 N/A – 2 386 1 4 386–395 2 3

CpP3004

EU593474

(AGAT)

(ACCT)

148 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP3211

EU593479

(AAAC)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP3215

EU593482

(AGAT)

385 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

Conserv Genet (2009) 10:935–954 951

123

Table 3 continued

Locus accession Repeat motif C .crocodylus C. latirostris M. niger P. palpebrosus C. yacare A. sinensis

Range (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KNRange (bp) KN

CpP3216

EU593483

(ACAG)

140 1 3 154 1 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP3217

EU593484

(AAAC)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP3220

EU593486

(AAAC)

103–107 2 3 184 1 2 125 1 3 98 1 2 N/A – 4 N/A – 3

CpP3303

EU593488

(AACC)

N/A – 3 355 1 2 355 1 3 353–361 2 2 N/A – 4 367 1 3

CpP3309

EU593490

(AGAT)

190–210 5 3 157–161 2 2 177–185 3 3 185–190 3 2 159–200 5 4 155–202 3 3

CpP3313

EU593491

(AGAT)

369–377 2 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP3314

EU593492

(AGAT)

303 1 3 303 1 2 307 1 3 298–323 3 2 303 1 4 303–305 2 3

CpP3601

EU593503

(AAC)

N/A – 3 N/A – 2 N/A – 3 156–162 2 2 N/A – 4 170–189 4 3

CpP3603

EU593504

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A 3

CpP4004

EU593510

(AGAT)

357–411 3 3 355–436 2 2 382 1 3 399 1 2 N/A – 4 N/A – 3

CpP4006

EU593511

(AGAT)

95 1 3 N/A – 2 N/A – 3 107 1 2 N/A – 4 N/A – 3

CpP4010

EU593513

(ACAT)

200 1 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP4013

EU593514

(AAAG)

352 1 3 353 1 2 353 1 3 N/A – 2 352 1 4 351–352 2 3

CpP4116

EU593518

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP4208

EU593520

(AGAT)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

CpP4301

EU593522

(ACT)

337–340 2 3 337 1 2 273–335 3 3 358 1 2 N/A – 4 260–345 3 3

CpP4304

EU593524

(AAC)

N/A – 3 N/A – 2 N/A – 3 N/A – 2 N/A – 4 N/A – 3

952 Conserv Genet (2009) 10:935–954

123

ﬁndings support those found for cross-species ampliﬁcation

within Caiman spp. (Zucoloto et al. 2002), as well as

within avian cross-species ampliﬁcation studies (Primmer

et al. 1996,2005). Although less frequent heterologous

microsatellite ampliﬁcation was observed in Alligatoridae

species, the new microsatellites presented here, together

with already existing genetic markers (Glenn et al. 1998;

Zucoloto et al. 2002,2006) provide an array of genetic

markers to support future research in Alligator and Caiman

species.

Allele numbers and ranges are presented in Table 2for

Crocodilidae species and Table 3for Alligatoridae species,

although these statistics are incomplete given the small

sample numbers available for some species. While several

loci were identiﬁed as being monomorphic, it would be

premature to assume that these loci are truly monomorphic,

due to low sample numbers. It is, however, recommended

that these microsatellites be considered and evaluated more

extensively for polymorphic information content in

respective target species. On the other hand, loci exhibiting

unique ﬁxed alleles for different species present the

potential for their employment in species identiﬁcation

kits, whereby suites of microsatellites could be used to

identify genetic proﬁles unique to speciﬁc species. This

could be a valuable tool for addressing problems associated

with hybridization (where morphological characteristics

are insufﬁcient), as well as for regulation of illegal skin

trade and wildlife forensics.

By far the most valuable outcome of this investigation is

the observed high level of cross-ampliﬁcation among true

crocodilians, providing many polymorphic microsatellites

for a range of Crocodylid species previously lacking

informative genetic markers. Once these markers are more

thoroughly characterised in speciﬁc populations, they will

help contribute to the evaluation of genetic diversity in a

wide range of crocodilians and help support conservation

and management efforts worldwide.

Acknowledgements This research was supported by Rural Indus-

tries Research and Development Corporation grant US-139A to the

University of Sydney. All research took place at the University of

Sydney, Australia, and the Savannah River Ecology Laboratory

(SREL), of the University of Georgia, USA. We thank Dr. Kent Vliet,

Dr. Robert Godshalk, Mitch Eaton and Matthew Shirley who kindly

provided us with many of the crocodilian DNA samples included in

this investigation.

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MANEJO, CONSERVACIÓN Y APROVECHAMIENTO DE COCODRILOS EN ÁREAS NATURALES PROTEGIDAS: EL CASO DE LA RESERVA DE LA BIOSFERA SIAN KA’AN

Chapter

Sep 2021

Gonzalo Merediz Alonso

The capter presents a population study of Morelet's crocodile (Crocodylus moreletii) in Sian Ka'an Biosphere Reserve, Mexico. The results allow to modeling different harvesting scenarios of a wild population. The model shows that ranching can be a virtuous strategy that helps sustain and recover recover populations, as long as it includes the reintroduction to wildlife of a portion of the extracted individuals. If ranching also involves local communities, it can incentivize them to protect crocodile habitat inside and outside protected areas.

GENÉTICA DE LA CONSERVACIÓN DE LOS CROCODYLIA DE MÉXICO

Chapter

Full-text available

Oct 2021

TÓPICOS DE ESTUDIO Y CONSERVACIÓN DE LOS COCODRILOS EN MÉXICO

Book

Full-text available

Oct 2021

La presente obra es una compilación de temas básicos y fundamentales, de utilidad para los biólogos, profesionistas en conservación y personas dedicadas al estudio de los cocodrilos en México. Consideramos que, para estudiar los efectos de la interacción del ser humano con las poblaciones de cocodrilos, así como de las interacciones entre las poblaciones de cocodrilos con el ambiente, se debe llevar a cabo una serie de métodos que permitan obtener datos útiles que ayuden a la conservación de estas especies. En este libro mostramos los enfoques y análisis más usados para evaluar aspectos demográficos, ecológicos y genéticos en las poblaciones de cocodrilos, así como estrategias para conservar a estas especies. Para esta obra se contó con la participación de destacados investigadores adscritos a diferentes instituciones académicas, gubernamentales y de ong del país, así como de expertos en la materia que colaboraron para integrar este documento, que es sólo un breve acercamiento al estudio y conservación de los cocodrilos, tocando temas diversos que incluyen la investigación, el manejo, la docencia y la divulgación. El libro se divide en dos apartados, el primero lo integran cuatro temas en los que se aborda información sobre la taxonomía, biología, importancia ecológica y cultural de los cocodrilos, así como temas de legislación útiles para su protección y aprovechamiento. Estos temas permiten tener una visión general de estos aspectos básicos pero necesarios en el planteamiento de estudios y estrategias de conservación y aprovechamiento sustentable. El segundo apartado, contiene cinco temas enfocados principalmente al diseño y aplicación de las técnicas de estudio para evaluar aspectos de bioacústica, densidad poblacional y la dinámica de las poblaciones de cocodrilos, así como su estructura genética. También se abordan de manera general las técnicas de conservación ex situ, así como el manejo y aprovechamiento de cocodrilos en áreas naturales protegidas.

Conservation Genetics of New World Crocodilians

Book

Nov 2020

This book aims to be a comprehensive review of the literature on the conservation genetics of the New World crocodilians, from the biological and demographical aspects of the living species to the application of molecular techniques for conservation purposes. It covers the current status of the molecular genetics applied to phylogenetics, phylogeography, diversity, kinship and mating system, and hybridization, as well its implications for decision making with regards to the conservation of these species at academic and governmental levels. This book can be used as a guide for graduate and undergraduate students to understand how conservation genetics techniques are carried out and how they can help preserve not only crocodilians but also other living species.

Poligame Nylkrokodille (Crocodylus niloticus) op ŉ krokodilplaas: Vrugvliese vertel die storie

Article

Full-text available

Nov 2020

Meer as een vaar in ’n krokodilbroeisel verhoog die effektiewe populasiegrootte en lei tot ’n stadiger verlies van genetiese variasie as gevolg van inteling en lukraak genetiese swerwing. Meer as een vaar kan ook die variasie met betrekking tot eienskappe wat van kommersiële belang is tussen krokodille uit dieselfde broeisel verklaar. Vrugvliese kan ’n nie-ingrypende bron van DNS verskaf waarmee die genotipe van Nylkrokodilbroeilinge (Crocodylus niloticus) bepaal kan word. Die doel van hierdie studie was om vas te stel hoe doeltreffend die genotipe van Nylkrokodilbroeilinge uit die vrugvliese wat in uitgebroeide eiers agterbly bepaal kan word en of ’n broeisel uit ’n kommunale teeldam op ’n kommersiële plaas meer as een vaar kan hê. Elf mikrosatellietloki is gebruik om die DNS-profiele van 4–6 (gemiddeld 4.4) vrugvliesmonsters (VVMe) van elk van 25 broeisels uit dieselfde teeldam op ’n kommersiële Nylkrokodilplaas te bepaal. DNS het op al 11 loki in 95 van die 110 individue vermeerder, op 1–10 loki in 13 en op geen lokus nie in twee. Drie tot 20 allele is per lokus gevind. Afsonderlike beoordeling van loki het getoon dat 13 broeisels minstens twee vaars gehad het. Met ’n multilokusprogram (Colony) is afgelei dat 19 broeisels minstens twee vaars gehad het, en dat poliandrie en poliginie algemeen was. Verdere navorsing is nodig om die nuttigheid van vrugvliese as ’n bron van DNS vir nesse uit die natuur te bepaal en om, deur meer VVMe per broeisel te gebruik, die mate van poliandrie en poliginie op Nylkrokodilplase en in die natuur meer presies te bepaal.

Historical Perspective, Distribution, Ecology and Population Genetics of Saltwater Crocodile (Crocodylus porosus Schneider, 1801) in Sarawak, Malaysian Borneo

Thesis

Oct 2019

Mohd Izwan Zulaini Abdul Gani

This study is designed to gather information on historical exploitation and ongoing HCC; recent distribution and ecology of crocodile and genetic relationship of crocodile population in Sarawak, to aid sustainable crocodile management and finding solutions for mitigating the HCC. Historical data saw a connection between the exploitation of crocodile with decreasing trend of HCC in Sarawak from the Rajah Brooke era (1900 – 1941) until the post-war period (1946 – 1979), and an increasing trend of HCC from 1980 until 2017 in response to the recovery of the animal populations. Since 1900, crocodile attacks had been occurred in 22 major river basins (RB) in Sarawak, suggesting that the reptile has been widely dispersed throughout all major river basins in the state. For 118 years (1900 – 2017), the highest number of crocodile attacks were recorded in Lupar RB (22.2%) and the attacks had happened up to the inland areas of Belaga and Pelagus in Rajang RB. Further analysis of incidents show crocodile attacks were associated with the human activities pattern, where more attacks involved male victims (84.4%) and adults from age 31 to 40 years old (19.3%). The data also revealed that crocodile attacks in Sarawak could happen anytime regardless of the time, month, season, lunar cycle or tidal. However, more attacks were recorded during the daylight, in the months of March and April, during the Northeast monsoon, at the nights of the first quarter of the lunar cycle and at the time of high tide. Furthermore, fishing (25.2%) and bathing (24.4%) possess the highest risk of crocodile attack in Sarawak, clearly showed that crocodiles are more likely to attack when the victim is in water. Crocodile survey in selected tributaries in Rajang RB showed the distribution of the reptiles throughout the river basin with higher crocodile density at the lower region, the highest density was in Igan River (1.37 individuals/km); while in the middle and upper regions had recorded relatively low density with the lowest density recorded was in Katibas River (0.06 individuals/km) and no crocodile was spotted in Kanowit River. Four out of eight surveyed rivers in Rajang RB recorded increase in the density of crocodile compare to previous survey suggesting that the crocodile population in the river basin is experiencing recovery. The presence of crocodile in different regions (lower, middle and upper) of Rajang RB indicated that C. porosus in Sarawak live in wide range of habitats; from large salt water river system and small tidal tributaries (near to estuary) in lower region into hypo-saline or fresh water non-tidal tributaries in the middle and upper regions. Variation in term of density and distribution of crocodile between the different regions are mainly influenced by the saline characteristic of the river, habitats and the abundance of food sources for crocodile. Based on the analysis of DNA microsatellite sequence data, distinctive subpopulations of C. porosus according to geographical area (river basin) could be observed. High gene flow (Nm) among the crocodile subpopulations suggests frequent movements of the reptile happen across the river basins throughout Sarawak. In general, populations of C. porosus in Sarawak are experiencing expansion as supported by the mismatch distribution and evolutionary neutrality test data, suggesting that populations of crocodile in Sarawak are panmictic population. The findings of the present study imply that increasing of crocodile attacks is associated with the recovery and increased distribution of the reptile in Sarawak, thus crocodile management should emphasis on mitigating HCC and simultaneously continue the efforts for conservation of crocodile and its habitat. Keywords: Crocodylus porosus, human-crocodile conflict, recovery, expansion.

Characterization of 25 new microsatellite markers for the green turtle (Chelonia mydas) and cross-species amplification in other marine turtle species

Article

Full-text available

Mar 2023
MOL BIOL REP

Background The green sea turtle, Chelonia mydas, is a migratory species with a strong natal homing behavior leading to a complex population structure worldwide. The species has suffered severe declines in local populations; it is therefore crucial to understand its population dynamics and genetic structure to adopt appropriate management policies. Here, we describe the development of 25 new microsatellite markers specific to C. mydas and suitable for these analyses. Methods and results They were tested on 107 specimens from French Polynesia. An average allelic diversity of 8 alleles per locus was reported and observed heterozygosity ranged from 0.187 to 0.860. Ten loci were significantly deviant from the Hardy-Weinberg equilibrium, and 16 loci showed a moderate to high level of linkage disequilibrium (4–22%). The overall Fis was positive (0.034, p-value < 0.001), and sibship analysis revealed 12 half- or full-sibling dyads, suggesting possible inbreeding in this population. Cross-amplification tests were performed on two other marine turtle species, Caretta caretta and Eretmochelys imbricata. All loci successfully amplified on these two species, though 1 to 5 loci were monomorphic. Conclusion These new markers will not only be relevant for further analyses on the population structure of the green turtle and the two other species, but they will also be invaluable for parentage studies, for which a high number of polymorphic loci are necessary. This can provide important insight into male reproductive behavior and migration, an aspect of sea turtle biology that is of critical importance for the conservation of the species.

Effective population size of broad-snouted caiman (Caiman latirostris) in Brazil: A historical and spatial perspective

Article

Jun 2021

Caiman latirostris has a large geographic distribution, that includes Argentina, Bolivia, Brazil, Paraguay, and Uruguay. In Brazil illegal hunting and land use change have caused population decline, relatively well documented in the last three decades. At such circumstances, the estimate of the species effective population size might help its viability analysis. Single-sample estimator has been developed to estimate current effective population size (Ne). Its main advantage over former methods is that it requires a single sampling, whereas temporal methods require at least two in distinct periods. Such method has been used to estimate Ne of broad-snouted caiman populations in the present study over representative areas of the species range in Brazil. As a result, we learned that in most populations only a relatively low number of adults effectively contribute to genetic variation. The following measures are proposed as management actions to mitigate such problem: (1) an update of population sampling on the main river basins where the species lives; (2) definition, delimitation and conservation of natural habitats for the conservation of the species in the wild, to guarantee its reproduction; and (3) new conservation genetic studies to determine current genetic diversity and its monitoring on the main river basins of the species range, with special attention to genetic diversity recovery.

Molecular Markers Applied to Conservation Genetics of American Crocodilians

Chapter

Nov 2020

The subject of this chapter is addressed seeking to establish a balanced relationship of deepening, trying to be interesting for those who are looking for information on molecular markers, while not intending to be too long in the descriptions of the techniques and providing an indication of application in molecular ecology of crocodilians that are best treated in other chapters of the book. Whenever possible, we use examples of the results of our own research with crocodilians, while mixing them with illustrative images of the techniques with the intention of making the reading interesting both for the public that wants to study other groups of living beings and for other researchers like us falling in love with crocodilians. The application of molecular markers in molecular ecology is presented in the next chapters: a discussion of the progress in phylogenetic studies is done in Chap. 3; the application of molecular markers to study phylogeography is presented in Chap. 4; a more accurate review of the molecular markers used to conservation genetics studies is done in Chap. 5; in Chap. 6 parentage and mating systems of crocodilians are reviewed in the light of molecular markers; and in Chap. 7, examples of hybridization detected with those markers were depicted. A review of the development of molecular markers for later use in the studies of molecular ecology of crocodilians in America is presented in this chapter, from the first studies with isoenzymes to the most current techniques.

Genetic Diversity of New World Crocodilians

Chapter

Nov 2020

Genetic diversity is one of the most important attributes of any population; it is defined as the variation in the amount of genetic information within and among individuals of a population, species, assemblage, or community. It can be expressed as differences between individuals at different levels, such as morphological features, structure and chromosomal number, and polymorphisms of sequences of DNA or proteins. An assessment of genetic diversity is fundamental to population genetic studies and has extremely important applications in conservation biology and the development of management and sustainable use plans. This chapter discusses the main indices that allow analyzing genetic variability and population structure of New World crocodilian populations, the methodologies used to estimate these indices, and the principal population genetic data available for these species. The effective population size concept is also discussed, a fundamental parameter in the study of principally those crocodile populations that have been drastically reduced in size and/or suffered fragmentation of their environments.

Characterization of Microsatellite DNA Loci in American Alligators

Article

Full-text available

Aug 1998
COPEIA

Microsatellite loci of American alligators were identified from small insert DNA libraries. The average length of microsatellites (18.4 repeats) was similar to that observed in mammals. Polymerase chain reaction (PCR) primers were developed and tested for 20 microsatellite loci that contained at least 10 uninterrupted AC or AG repeats. Genotypes for the 15 loci that could be scored readily were obtained for alligators from Louisiana and Florida. Eleven of the 15 loci were polymorphic. For the polymorphic loci, the number of alleles per locus ranged from 4-17 (average = 8.5), and observed heterozygosity within populations ranged from 0.231-0.865 (average = 0.466). Heterozygosity of these loci is almost 20 times higher than values obtained using isozymes. Populations from Louisiana and Florida differed substantially at these loci (overall F_ST=0.137,θ _p=0.239, and R_ST=0.387). The PCR primers also produced single amplicons from species of Alligatoridae, Gavialidae, and Crocodilidae, indicating that they may be useful for genetic studies in other crocodilians.

Cross-species microsatellite amplification in South American Caimans (Caiman spp and Paleosuchus palpebrosus)

Article

Full-text available

Jan 2006
GENET MOL BIOL

Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral character-istics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Cai-man latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.

Microsatellites in Morelet's Crocodile (Crocodylus moreletii) and Their Utility in Addressing Crocodilian Population Genetics Questions

Article

Full-text available

Sep 2001

Genetic Diversity, Population Subdivision, and Gene Flow in Morelet's Crocodile (Crocodylus moreletii) from Belize, Central America

Article

Full-text available

Dec 2002

The lack of information surrounding natural history and ecology of the endan- gered Morelet's crocodile (Crocodylus moreletii) has prompted a baseline study of the population genetics for this species. Nine microsatellite loci have been used to estimate genetic structure within and gene flow patterns among crocodiles (using a recently described maximum likelihood approach) from seven localities in north- central Belize. Individuals from the seven localities grouped into four apparent pop- ulations. Within localities, a high degree of genetic heterogeneity was observed. Among all localities, some subdivision was present (F ST 5 0.062; RST 5 0.100). Fur- thermore, among the apparent populations, we found a significant correlation be- tween geographic distance and genetic subdivision. Our findings suggest a relatively high level of migration among populations (Nm 5 5.15) and are consistent with an isolation-by-distance model of gene flow. Two contiguous subpopulations in partic- ular, New River and New River Lagoon, may form an important source for genetic variation for smaller populations throughout the region. These data will allow us to test hypotheses of relatedness among C. moreletii for other drainages in Belize and will be useful in optimizing future management programs for C. moreletii.

Low Levels of Nucleotide Diversity in Crocodylus moreletii and Evidence of Hybridization with C. acutus

Article

Full-text available

Aug 2004

Examinations of both population genetic structure and the processes that lead to such structure in croc-odilians have been initiated in several species in response to a call by the IUCN Crocodile Specialist Group. A recent study used microsatellite markers to characterize Morelet's crocodile (Crocodylus moreletii) populations in north-central Belize and presented evidence for isolation by distance. To further investigate this hypothesis, we sequenced a portion of the mitochondrial control region for representative animals after including samples from additional locales in Belize, Guatemala and Mexico. While there is limited evidence of subdivision involving other locales, we found that most of the differentiation among populations of C. moreletii can be attributed to animals collected from a single locale in Belize, Banana Bank Lagoon. Furthermore, mitochondrial DNA sequence analysis showed that animals from this and certain other locales display a haplotype characteristic of the American crocodile, C. acutus, rather than C. moreletii. We interpret this as evidence of hybridization between the two species and comment on how these new data have influenced our interpretation of previous findings. We also find very low levels of nucleotide diversity in C. moreletii haplotypes and provide evidence for a low rate of substitution in the crocodilian mito-chondrial control region. Finally, the conservation implications of these findings are discussed.

Microsatellite markers for Crocodylus: new genetic tools for population genetics, mating system studies and forensics

Article

Full-text available

Jan 2011

ABSTRACT Questions of population identification and gene flow have become more important in the conservation and management of crocodilians. Additionally there has long been an interest in understanding crocodilian mating systems. To address such questions we designed nuclear microsatellite markers from the DNA of C. acutus, C. porosus and C. johnstoni. We report on the development and testing of 26 new microsatellite loci for Crocodylus spp, which represent the first microsatellite loci found in Crocodylus.

Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment

Article

Jan 2007

Cross-species amplification of microsatellite loci in aphids: Assessment and application

Article

Mar 2004
MOL ECOL NOTES

Despite the relative ease of isolating microsatellites, their development still requires substantial inputs of time, money and expertise. For this reason there is considerable interest in using existing microsatellites on species from which markers were not cloned. We tested cross-species amplification of 48 existing aphid loci in species of the following genera: Aphidinae: Aphidini: Aphis and Rhopalosiphum; Aphidinae: Macrosiphini: Acyrthosiphum, Brevicoryne, Diuraphis, Illinoia, Macrosiphoniella, Macrosiphum, Metopeurum, Metapolophium, Myzus, Phorodon, Sitobion and Uroleucon and Neuquenaphidinae: Neuquenaphis. Our results show cross-species application of known microsatellite loci is a highly promising source of codominant markers for population genetic and evolutionary studies in aphids.

Factors affecting avian cross‐species microsatellite amplification

Article

Jul 2005
J AVIAN BIOL

Compilation and analysis of information from the literature regarding cross-species microsatellite amplification and polymorphism success, and relating this to source-target species genetic distance as estimated by pairwise cytochrome b (cytb) divergence, enabled an in-depth investigation of factors affecting avian cross-species microsatellite amplification. Source-target species cytb distances provided accurate estimates of cross-species microsatellite amplification/polymorphism success rates not only in birds, but also in taxa where microsatellites cross-amplify across contrasting levels of taxonomic classification (frogs and cetaceans). As cytb is one of the most commonly sequenced DNA regions, pairwise cytb genetic distances should therefore be useful for predicting cross-species microsatellite success across a range of taxonomic groups. While the most important factor affecting cross-species microsatellite amplification/polymorphism success was a negative association with source-target species genetic distance, associations with additional features affecting cross-species amplification/polymorphism success included: decreasing PCR annealing temperature significantly increasing the chance of successful cross-species amplification, and a significant positive association between source species polymorphism and the proportion of target species in which a locus revealed polymorphism. No association between cross-species amplification and repeat motif (di-, tri-, or tetranucelotide) or repeat structure (perfect, imperfect, or compound) was observed. A set of nine loci which cross-amplified across an unusually broad range of passerine bird species were also identified, and could serve as a good starting point for cross-species amplification testing in passerine species for which insufficient loci are available.

The Concervation of Dinucleotide Microsatellites among Mammalian Genomes Allows the Use of Heterologous PCR Primer Pairs in Closely Related Species

Article

Aug 1991

The high degree of polymorphism displayed by DNA microsatellites makes them useful as DNA markers in linkage studies. A search of the DNA sequence databases revealed that the locations of dinucleotide microsatellites are often conserved among mammalian species, enabling the prediction of the presence of DNA microsatellites using comparative genetic data. In closely related species such as cattle and sheep, this conservation was close enough to allow PCR primers designed for use in one species to be used to analyze microsatellite length polymorphism in the other. A total of 48 sets of primer pairs, flanking bovine microsatellites and giving polymorphic PCR products in that species, were tested with template DNA from sheep, horses, and humans. Specific products were obtained in 27 cases (56%) with ovine DNA, 20 of which (42%) showed polymorphisms. With equine DNA, 3 (6.2%) gave specific but monomorphic products, while no specific products were obtained using human DNA. The ability to use heterologous PCR primers, coupled with comparative mapping information will facilitate the use of DNA microsatellites in gene mapping studies in closely related species such as cattle and sheep, rat and mouse, or primates.

Cross-species amplification of microsatellites in crocodilians: Assessment and applications for the future

Abstract and Figures

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