The divergence of two independent lineages of an endemic Chinese gecko,Gekko swinhonis,launched by the Qinling orogenic belt

The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual‐based phylogenetic analyses of nucDNA and Bayesian‐clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male‐biased dispersal in this species. High genetic divergence, long‐term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species.     

Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major: evidence from phylogeographic analysis and ecological niche models

Different scales and frequencies of glaciations developed in Europe and Asia during the Pleistocene. Because species’ responses to climate change are influenced by interactive factors including ecology and local topography, the pattern and tempo of species diversification may vary significantly across regions. The great tit Parus major is a widespread Eurasian passerine with a range that encircles the central Asian desert and high‐altitude areas of the Tibetan Plateau. A number of genetic studies have assessed the effect of paleo‐climate changes on the distribution of the European population. However, none have comprehensively addressed how paleo‐climate change affected the distribution of the great tit in China, an apparent hotspot of P. major subspecific diversity. Here, we describe likely paleo‐climatic effects on P. major populations in China based on a combination of phylogeography and ecological niche models (ENMs). We sequenced three mitochondrial DNA markers from 28 populations (213 individuals), and downloaded 112 sequences from outside its Chinese range. As the first step in clarifying the intra‐specific relationships among haplotypes, we attempted to clarify the divergence and demography of populations in China. Phylogeographic analysis revealed that P. major is comprised of five highly divergent clades with geographic breaks corresponding to steep mountains and dry deserts. A previously undescribed monophyletic clade with high genetic diversity, stable niches and a long and independent evolutionary history was detected in the mountainous areas of southwest China. The estimated times at which these clades diverged was traced back to the Early‐Middle Pleistocene (2.19–0.61 mya). Contrary to the post‐LGM (the Last Glacial Maximum) expansion of European populations, demographic history indicates that Asian populations expanded before the LGM after which they remained relatively stable or grew slowly through the LGM. ENMs support this conclusion and predict a similar distribution in the present and the LGM. Our genetic and ecological results demonstrate that Pleistocene climate changes shaped the divergence and demography of P. major in China.     

Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood, and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best‐fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best‐fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers. In contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features and more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.     

Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust

The migratory locust, Locusta migratoria, is the most widely distributed grasshopper species in the world. However, its global genetic structure and phylogeographic relationships have not been investigated. In this study, we explored the worldwide genetic structure and phylogeography of the locust populations based on the sequence information of 65 complete mitochondrial genomes and three mitochondrial genes of 263 individuals from 53 sampling sites. Although this locust can migrate over long distances, our results revealed high genetic differentiation among the geographic populations. The populations can be divided into two different lineages: the Northern lineage, which includes individuals from the temperate regions of the Eurasian continent, and the Southern lineage, which includes individuals from Africa, southern Europe, the Arabian region, India, southern China, South‐east Asia and Australia. An analysis of population genetic diversity indicated that the locust species originated from Africa. Ancestral populations likely separated into Northern and Southern lineages 895 000 years ago by vicariance events associated with Pleistocene glaciations. These two lineages evolved in allopatry and occupied their current distributions in the world via distinct southern and northern dispersal routes. Genetic differences, caused by the long‐term independent diversification of the two lineages, along with other factors, such as geographic barriers and temperature limitations, may play important roles in maintaining the present phylogeographic patterns. Our phylogeographic evidence challenged the long‐held view of multiple subspecies in the locust species and tentatively divided it into two subspecies, L. m. migratoria and L. m. migratorioides.     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

Hidden in the Arabian Mountains: Multilocus phylogeny reveals cryptic diversity in the endemic Omanosaura lizards

An increase in studies in the Hajar Mountains from the southeastern Arabian Peninsula has revealed a high richness of endemic evolutionary lineages with many cryptic taxa. Omanosaura is the only lacertid lizard genus endemic to the Hajar Mountains, with two species O. cyanura and O. jayakari distributed throughout this mountain range. The phylogenetic relationships and genetic diversity between and within these species have been poorly studied. In this study, we collected mitochondrial (12S, cytb, and nd4) and nuclear (cmos and mc1r) sequences for 25 specimens of Omanosaura, including 15 individuals of O. jayakari and 10 of O. cyanura. We performed phylogenetic analyses based on network reconstruction, maximum likelihood and Bayesian inference to estimate the relationships and intraspecific genetic diversity of these species. We estimated the time of divergence between the two species in the Miocene, around 8.5 million years ago. Omanosaura jayakari shows little genetic diversity, while O. cyanura presents two differentiated lineages. These are reciprocally monophyletic at mitochondrial and nuclear genes and present a high genetic distance between them. These two lineages are associated with the geographic features of the Hajar Mountains, with one lineage distributed in the northernmost part of the Hajar Mountains and the other in the rest of the western Hajars, the Jebel Akhdar, and the eastern Hajars. This geographic relationship has been recovered previously in other reptile taxa and is generally associated with high levels of local genetic diversity. Our results suggest the existence of cryptic diversity within O. cyanura and support a general biogeographic pattern of high diversity and endemism in the northern Hajar Mountains that certainly deserves additional research in the future.     

Phylogeography of the fiscal shrike (Lanius collaris): a novel pattern of genetic structure across the arid zones and savannas of Africa

Aim Savanna occupies a substantial part of Africa, being distributed around the two major tropical rain forest blocks in what is referred to as the Savanna Belt. Our current understanding of the genetic structure within species distributed across the Savanna Belt is primarily derived from mammalian taxa, studies of which have revealed a suture zone or transition between northern and east/southern Africa clades in south‐western Kenya and north‐western Tanzania. We conduct a phylogeographic study of the fiscal shrike (Lanius collaris), a polytypic species distributed across the Savanna Belt of Africa and for which morphological and vocal data are in agreement with the suture zone recovered for mammalian taxa, to test the hypothesis of a spatially congruent genetic break across several taxa, including birds. Location Africa, south of the Sahara. Methods We analysed DNA sequences recovered from four loci (one mitochondrial, two autosomal and one Z‐linked) in 66 individuals, representing all recognized subspecies, as well as putatively closely related species. We make use of a combination of tree‐building and population genetic methods to investigate the phylogeographic structure of the fiscal shrike across Africa. Results The fiscal shrike consists of two primary lineages with a strong geographic component: a northern group distributed from southern Tanzania to Senegal, and a southern group distributed from Botswana/Zambia to South Africa with isolated populations in Tanzania and northern Malawi. Unexpectedly, Souza’s shrike (L. souzae) was nested within L. collaris, as the sister group of the southern group. The positions of Mackinnon’s shrike (L. mackinnoni) and that of the São Tomé shrike (L. newtoni) were variable, being either nested within the fiscal shrike or sister to the L. collaris–L. souzae clade. Our divergence time analyses suggest that the Lanius collaris species complex started to diversify around 2.2 Ma. Main conclusions Our study reveals a distinct biogeographic pattern for a savanna distributed species in Africa, with the transition between the two primary genetic lineages occurring at a latitude of c. 15–16° S, 10° S further south than shown elsewhere for several mammalian species.     

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes)

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median‐joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum.     

Multiple dispersal out of Anatolia: biogeography and evolution of oriental green lizards

The oriental green lizards of the Lacerta trilineata group are widely distributed in Greece, Anatolia, the eastern Mediterranean, the southern Caucasus, and the Zagros mountains in Iran. We studied their phylogeography using three mitochondrial markers with comprehensive sampling from most representatives of the group. Their phylogeny and divergence times (implementing fossil‐based molecular clock calibrations) were inferred using Bayesian methods, and haplotype networks were reconstructed to assess how genetic diversity and current distributional patterns were shaped. According to our phylogenetic analyses, the group constitutes a well‐supported monophylum containing several distinct evolutionary lineages with high haplotype diversity. Vicariance might explain the divergences within most lineages that have accumulated by range restriction and expansion of populations as a result of Quaternary climate oscillations and glacial refugia. However, niche divergence appears to be a major force promoting speciation, and large scale distributional patterns between lineages were shaped earlier by multiple, independent dispersals out of Anatolia during the Pliocene and early Pleistocene. The results of the present study also suggest that the group is in need of a taxonomical revision because the identified lineages and genetic diversity are not congruent with the currently recognized subspecies. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 398–408.     

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush‐tailed rock‐wallaby (Petrogale penicillata; n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush‐tailed rock‐wallabies, whose divergence appears to date to the mid‐Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north–south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush‐tailed rock‐wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.     

A TEST OF THE GLACIAL REFUGIUM HYPOTHESIS USING PATTERNS OF MITOCHONDRIAL AND NUCLEAR DNA SEQUENCE VARIATION IN ROCK PTARMIGAN (LAGOPUS MUTUS)

The glacial refugium hypothesis (GRH) proposes that glaciers promoted differentiation and generation of intraspecific diversity by isolating populations in ice-free refugia. We tested three predictions of this hypothesis for the evolutionary divergence of rock ptarmigan (Lagopus mutus) during the Wisconsin glaciation of the late Pleistocene. To do this, we examined subspecies distributions, population genetic structure, and phylogenetic relationships in 26 populations across North America and the Bering Sea region. First, we analyzed sequence variation in the mitochondrial control region, in a nuclear intron (Gapdh), and in an internal transcribed spacer (ITS1). Control region sequences of 154 rock ptarmigan revealed strong population and phylogeographic structure. Variation in intron sequences of 114 rock ptarmigan also revealed significant population structure compatible with results for the control region. Rock ptarmigan were invariant for ITS1. Second, we show that five known Nearctic refugia and an Icelandic refugium are concordant with the current distribution of morphologically distinct subspecies; five of these six refugia are geographically concordant with the distribution of closely related control region haplotypes. Third, our estimates of the time since phylogenetic lineages diverged predated the last glacial maximum for all but two lineages. In addition, all lines of evidence suggest that two unknown refugia in the Bering Sea region supported rock ptarmigan during the Wisconsin glaciation. Overall, our results are most consistent with the hypothesis that isolated populations of rock ptarmigan diverged in multiple refugia during the Wisconsin and that geographic variation reflects patterns of recolonization of the Nearctic after the ice receded. The GRH may therefore offer the most plausible explanation for similar biogeographic patterns in a variety of Nearctic vertebrates.     

Divergent sympatric lineages of the Atlantic and Indian Ocean crinoid Tropiometra carinata

The shallow water comatulid crinoid Tropiometra carinata is native to both the Atlantic and Indian Oceans, a distribution anomalous among shallow water crinoids and many other broadcast spawning species. Given this species' short pelagic larval duration, the findings of previous work that suggest that the Benguela upwelling is a significant barrier to gene flow in broadcast spawning species, and T. carinata's unexpected geographic distribution, we predicted that the crinoids presently recognized as T. carinata consisted of a species complex. To test this prediction, we sequenced a portion of the mitochondrial cytochrome oxidase 1 gene from 30 individuals of T. carinata collected from Brazil, the Mozambique Channel, Madagascar, and Reunion Island. We found that nucleotide divergence ranged 0.02–3.10% among haplotypes. Moreover, while a Bayesian phylogenetic tree indicated that there were two substantially divergent genetic lineages, there was no evidence to support that T. carinata is comprised of a species complex due to isolation‐by‐distance. Surprisingly, both lineages were found in sympatry in both the Atlantic and Indian Oceans. Likewise, a 95% parsimony haplotype network revealed that identical haplotypes are found in both oceans, suggesting that a species complex may indeed exist, just not one caused by geographic isolation. We discuss possible explanations for this unexpected genetic structure, such as natural dispersal or human‐mediated movement, and how the genetic structure found here is relevant to other marine organisms and to cryptic speciation.     

Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia,introgression and riverine barriers

The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest species, we analysed morphological characters, mitochondrial DNA sequences and nuclear microsatellite loci in the Silver Pheasant (Lophura nycthemera). In a pattern generally consistent with phenotypic clusters, but not nominal subspecies, deeply divergent mitochondrial lineages restricted to different geographic regions were detected. Coalescent simulations indicated that the time of main divergence events corresponded to major glacial periods in the Pleistocene and gene flow was only partially lowered by drainage barriers between some populations. Intraspecific cytonuclear discordance was revealed in mitochondrial lineages from Hainan Island and the Sichuan Basin with evidence of nuclear gene flow from neighbouring populations into the latter. Unexpectedly, hybridization was revealed in Yingjiang between the Silver Pheasant and Kalij Pheasant (Lophura leucomelanos) with wide genetic introgression at both the mtDNA and nuclear levels. Our results highlight a novel phylogeographic pattern in a subtropical area generated from the combined effects of climate oscillation, partial drainage barriers and interspecific hybridization. Cytonuclear discordance combined with morphological differentiation implies that complex historical factors shaped the divergence process in this biodiversity hot spot area of southern China.     

Song evolution in the coal tit Parus ater

Since in oscine birds song divergence often leads to premating reproductive isolation, we asked which factors drive the evolution of song in a widespread species, the coal tit Parus ater. Based on an almost taxon‐complete phylogeny we correlated song divergence with morphometric (ecology), genetic (time), and geographic distances (separation). We found eight well‐supported mitochondrial lineages, one of which consists of melanolophus (usually treated as a separate species) and whose relationships remain generally unresolved. Due to intense song variability even sophisticated sonametric analyses failed to separate sub‐specific units. We tested for the role of song in reproductive isolation by playing songs from China and the Himalayas to Central European males. They recognize them as conspecific, but react to their playbacks less aggressively than to local songs. While morphological divergence is correlated with neither time nor separation, song divergence coincides more with geographic than genetic distance. This is mainly driven by differences along longitude and is especially prominent in the southern part of the species’ range, where six lineages persisted during the last glaciation while the north was subsequently re‐occupied by two lineages.     

Glacial vicariance and historical biogeography of rock ptarmigan (Lagopus mutus) in the Bering region

In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However, isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow. In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.     

Genetic diversity of the naked mole‐rat (Heterocephalus glaber)

The naked mole‐rat (Heterocephalus glaber) is used as an animal model in various studies, but not much is known on the genetic diversity of this animal. Here, on the basis of dataset collected from the most part of the distribution range of the naked mole‐rat, we reconstruct phylogenetic relationships between its different lineages using mitochondrial and nuclear markers. We also mapped the distribution of the main genetic lineages, dated the divergence using different Bayesian tree‐calibration techniques, and modeled the distribution of ecological niches for the period of last glacial maximum. Our results show the existence of two deeply divergent clades designated as the eastern clade (East Ethiopia) and the southern clade (South Ethiopia and North Kenya). Additional phylogeographic structure was demonstrated for each of these two clades. Divergence between these two main lineages dated back to the Middle Pleistocene (ca. 1.4–0.8 Mya) and may have been related to climate changes in Africa during the Mid‐Pleistocene Revolution. In light of substantial genetic differences between the eastern and southern lineages of the naked mole‐rat, these two clades can be considered as two deeply divergent subspecies or even as distinct species.     

Are subspecies useful in evolutionary and conservation biology?

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.     

SPECIATIONAL HISTORY IN A DIVERSE CLADE OF HABITAT-SPECIALIZED SPIDERS (ARANEAE: NESTICIDAE: NESTICUS): INFERENCES FROM GEOGRAPHIC-BASED SAMPLING

This paper summarizes the results of an initial effort to reconstruct the speciational history of cave spiders (Nesticus) from the southern Appalachian Mountains of eastern North America. The Appalachian Nesticus fauna includes a large series of about 30 species distributed across islandlike cave and montane habitats. Many of the species are geographically restricted; all of the species are found in allopatry. Observed patterns of morphological variation and biogeographic evidence suggest that species diversification in this lineage may have occurred recently, perhaps in response to Pleistocene climatic fluctuations. To address questions about the spatial and temporal dynamics of Nesticus speciation, while accounting for potential phylogenetic difficulties, I have gathered nuclear and mitochondrial DNA sequences for a sample of individuals from 81 populations representing 28 Nesticus species. Analyses of these data indicate that considerable genetic divergence exists within and among currently recognized morphological species. Consistent with relatively deep species divergences, most of which likely predate the Pleistocene, is a prevailing pattern of phylogenetic concordance between taxonomic species and monophyletic gene tree lineages. The few deviations from monophyly detected can be tentatively attributed to a peripatric mode of speciation. Although species limits as inferred by the molecular data are generally concordant with patterns of morphological continuity and discontinuity in genitalia, there is evidence to suggest that cryptic phylogenetic lineages exist within some morphologically continuous units. This observation, in combination with the general depth of species lineages, makes any argument about rapid evolution in Nesticus genitalic characteristics unnecessary.