Table S1.

Summary of comparative phylogeographic studies, including a brief description of the objectives or main questions analyzed,

molecular markers used, taxa included (with sampling size if available), and genetic statistics and analyses performed. Main results are

highlighted (see text for description of each example).

Objective / Molecular Genus or species Genetic Main results / conclusions Reference

question marker (# of samples) statistics /

analyses

Vicariance COIII Peromyscus eremicus NJ, ML, Concordant intraspecific Riddle et al.

hypothesis. Cyt b group (4 spp, 73 MP, SD phylogeographical patterns support three 2000b

Evaluation of the individuals); vicariant events (mid Pleistocene, late

evolution of the Chaetodipus baileyi Pliocene, and Pliocene, respectively).

Baja California group (2 spp, 51); C. Results show a history of biogeographic

Peninsular desert arenarius (36); and evolutionary independence in northern

biota across 12 Dipodomys merriami and southern regions of the Baja California

taxa. group (60); Peninsular desert.

Ammospermophilus

(30); Bufo punctatus

(44)
Comparison of Cyt b, CR Andropadus HD, BCD, Values of genetic diversity unique to each Smith et al.

phylogeographic tephrolaemus (32) ML, MT, region, as well as some diversity shared 2000

structure of Nectarina oritis (40) PD among regions.

endemic birds Identification of specific regions that

across mountains harbor evolutionary significant units

in Africa. (ESU’s).

Evaluation of

phylogenetic

diversity index

(PD) and levels of

endemism.

Testing concerted Cyt b Reithrodontomys KHT, Support for both hypotheses based on three Sullivan et al.

versus independent sumichrasti (43) LRT, ML, statistical complementary methods. 2000

responses of MP, PBT, Phylogeographical incongruence together

codistributed Results compared to RRTM with history of covicariance as responses

rodents to past those found in to past climatic and geologic events.

climatic Peromyscus

fluctuations. aztecus/P. hylocetes

 complex

Predicting location COII Gnarosophia DA, EPS, Snail phylogeography is consistent with Hugall et al.

of refugia based on bellendenkerensis GD, predictions from the models in relation to 2002

paleoclimate (121) MCMC, the location and size of Pleistocene-

modeling of a ML, NJ, Holocene climatic refugia, and also to

snail. Comparison with PCM, SD extinction and recolonization patterns.

lizards and frogs, e.g. Comparisons with vertebrate fauna

Litoria, revealed concordant as well as inconsistent

Gnypetoscincus, (species-specific) phylogeographical

Carphodactylus patterns.

Evaluation of the Plant: Legume: KHY, ML, Legume and its root nodule bacteria do not Parker et al.

biogeographic chloroplast Amphicarpaea (12) MP, NJ show parallel cladogenesis. 2004

history and trnL region, Bacteria: Different Bradyrhizobium lineages evolved

phylogeography of nuclear Bradyrhizobium (18) in association with other legumes and

a symbiotic ribosomal colonized Amphicarpaea species at distinct

relationship. ITS, histone times.

H3-D
 Bacteria:

16S rRNA,

23S, ITS

Testing of the ND2 Poecillia butleri (13) BA, GDV, A Plio-Pleistocene vicariant event Mateos 2005

hypothesis of a Poeciliopsis LRT, associated with geological activity caused

vicariant event presidionis (1), MCk, ME, divergence in three different lineages.

responsible for P. latidens (1), ML, MP, Divergence times were estimated with the

concordant P. fasciata (2), NJ use of molecular clocks, supporting that

divergences in two P. presidionis (2), divergences between species were a

freshwater fish P. tumeri (1) consequence of the same vicariant event.

species.

Evaluation of the Cyt b Apodemus flavicolis GD, GDV, Species have different phylogeographical Michaux et al.

effect of (98) ML, MP, patterns and different European Quaternary 2005

Quaternary climate A. sylvaticus (102) MSN, NJ, refuges.

changes on TD Different patterns observed are associated

sympatric rodent with the species-specific ecological

species. plasticity.
Evaluation of AFLP Veronica alpine (107), AMOVA, Concordant phylogeographical patterns as Albach et al.

evolutionary (genomic V. bellidioides (68) ffp, fpp, a result of similar environmental histories. 2006

history in closely DNA), V. copelandii (3) GD, GDS, Also, different phylogeographical patterns

related sympatric trnL intron, V. cusickii (11) MP, NJ, and Pleistocene refugial areas in each

species from alpine 3’ exon, V. nutans (3) PCoA northern Europe and northern North

habitats in northern trnL-trnF V. nipponica (1) America.

Europe and North V. stelleri (4) Diversification patterns associated with

America. V. wormoskjoldii (3) higher genetic structure and diversity in

Comparison of species from North America.

intercontinental

phylogeograpy.

Evaluation of the CR Geochelone nigra HD, MD, Geographical distance and genetic Ciofi et al.

effect of vicariance micros (631) GD, GDV, distinctiveness strongly associated, 2006

on colonization AMOVA, concordant with recent colonization

and dispersal in NCA, BA, events.

islands, in recently MiE, Evidence of chronological association

derived lineages PCoA between orogenic events (volcanic

and species with activity) and species evolution.

limited dispersal Identification and proposal of different

ability. taxonomic units.

Evaluation of the Cyt b Cellana ornata (302), AMOVA, Moderate to strong effects of the marine Goldstien et

effect of a marine C. radians (321), C. GD, GDS, barrier. al. 2006

barrier between the flava (85) HD, MSN, Concordant allopatric fragmentation

North and South NCA patterns across species.

islands in New

Zealand in three

limpet species.

Discerning the COX1 Desmognathus HD, MSN, Results indicate that an extremely isolated Bonett et al.

introduced or relict monticola (100) NCA population of the species was an 2007

status of a introduction.

population of an Conservation applications designed based

endemic on the results that this not native

amphibian species. population should be extirpated.

Phylogeographic Cyt b Hylomyscus denniae HD, HKY, Geological reconstructions helped decipher Huhndorf et

patterns of D-loop (21), Hybomys lunaris LRT, chronology of events. al. 2007
montane endemic (13), Lophuromys MCk, ML, Volcanic activity, phylogeographical

rodents in woosnami (20) MP, NJ patterns, and divergence times coincided

fragmented areas and revealed that biogeographical barriers

of east-central and fragmentation from eruptive events

Africa. shaped the diversification of the species.

Evaluation of CR I Gallirallus DA, EPS, Codistributed species, despite similar Kirchman and

historic population philippensis (21) GD, GDV, phenotypic variation within the islands, Franklin 2007

demography of Chalcophaps indica HD, HKY, have historical and biogeographical

three codistributed (25) MCMC, differences.

bird species in an Rhipidura spilodera ML, Results support the hypothesis of recent

archipelago. (17) MSN, colonization and subsequent expansion in

Tmrca two species.

Testing for Cyt b, Mammals (12-136): HABC The shared vicariance hypothesis is not Leaché et al.

simultaneous COIII, Ammospermophilus supported. 2007

vicariance across ATPase6, leucurus, Chaetodipus The structured genetic diversity observed

codistributed taxa ND1, ND2, arenarius, C. baileyi in this region is the result of two different
along the middle of ND4 Dipodomys merriami biogeographical events.

the Baja California Peromyscus eremicus,

Peninsula. Thomomys bottae

Reptiles (12-37):

Callisaurus

draconoides, Uta

stansburiana,

Phrynosoma

coronatum,

Sceloporus

zosteromus, Pituophis

catenifer,

Trimorphodon

biscutatus

Evaluation of Cyt b Myopus schisticolor AMOVA, Shared late Quaternary phylogeographical Fedorov et al.

Eurasian refugia, (100) DA, EPS, patterns across species. 2008

vicariant events, GD, HD, Successive range expansions and

and recolonization Comparison with a HKY, contractions shaped the historical

of boreal species. diverse array of boreal MCk, dynamics of the species’ shared

species across Eurasia MD, environment.

MJHN,

ML, NJ,

TD

Evaluation of Cyt b, 12S Liolaemus tenuis BA, GD, Concordant phylogeographical Victoriano et

concordant (144), L. pictus (82), HD, MA, associations in all three species: groups al. 2008

phylogeographical L. lemniscatus (52) MAST, consistent with bioclimatic zones.

patterns in partially MDS, Shared orogenic vicariant events and

overlapping lizard ML, MRP, consequent divergence in two species.

species, PRM, Identification of major refugial areas and

considering STA dispersal routes.

topography and

endemicity

Comparison of ND4, tRNA Saproscincus GD, SD, Complex phylogeographical patterns Moussalli et

spatial patterns of basiliscus (139), S. AMOVA, reflect persistence of large, structured al. 2009

population tetradactyla (35), S. DA, BA, populations in the central zone.

persistence and czechurai (38) PCM Support for a vicariant barrier separating

isolation in three northern and central regions.

skink species, to Species-specific characteristics shaped

evaluate late- species distributions: mid-Holocene warm-

Quaternary climate wet climate was restrictive for high-

fluctuation in the elevation species, whereas cool-dry glacial

Australian Wet maximum climate restricted more

Tropics. generalist and low-elevation species.

Abbreviations refer to: AMOVA=Analysis of Molecular Variance, BA=Bayesian analysis, BCD=Bray-Curtis distance, DA=Demographic

analyses (e.g., growth, mutation rates, etc), ENM=Ecological niche modeling, EPS=Effective population size, ffp=fixed private fragments,

fpp=polymorphic private fragments, GD=Genetic diversity (or nucleotide diversity), GDS=Genetic distance, GDV=Genetic divergence,

HABC=Hierarchical Bayesian model, HD=Haplotype divergence or diversity, HKY=Hasegawa-Kishino-Yaro model, KHT=Kishino-

Hasegawa-Templeton, KHY=Kishino-Hasegawa-Yano, LRT= Likelihood ratio test, MA=Multivariate analysis, MAST=Maximum

agreement trees, MCk=Molecular clock, MCMC=Metropolis-Hastings Markov Chain Monte Carlo, MD=Mismatch distribution, MDS=

Multidimensional scaling analysis, ME=Minimum evolution, MiE=Migration rate estimation, MJHN=Median-joining haplotype network,

micros=microsatellites, ML=Maximum likelihood, MP=Maximum parsimony, MRP=Maximum representation with parsimony,

MSN=Minimum spanning network, MT=Mantel test, NCA=Nested clade analysis NJ=Neighbour-joining, PBT=Parametric bootstrap test,

PCM=Paleoclimate modeling, PCoA=Principal coordinate/Principal component analysis, PD=Phylogenetic diversity, PRM=Pairwise

regressions models, RRTM= Randomization test of reconciled tree maps, SD=Sequence divergence (%), SPN=Statistical parsimony

network, STA=Supertrees, TD=Time of divergence, Tmrca=Time to most recent common ancestor.