Genus Myriopholis Hedges, Adalsteinsson & Branch, 2009.

The snake genus Myriopholis is distributed across Africa, the Arabian Peninsula, and southwest Asia. The majority of the species are found in sub-Saharan Africa, particularly in west, central, and east Africa. Myriopholis belongs to the tribe Myriopholini within the subfamily Leptotyphlopinae, which contains Old World leptotyphlopids. Molecular dating analyses suggest the Myriopholini lineage diverged from other Leptotyphlopinae around 84 Mya in the Late Cretaceous. The deepest-branching Myriopholis species sampled was M. longicauda from South and East Africa, indicating the genus may have originated in southern Africa. Other divergences date to around 60 Mya, suggesting dispersal of Myriopholis out of Africa into Arabia and Asia later in the Cenozoic after the initial radiation within Africa [53].

In Iran the genus is found on the southern slopes of the Central and Western Alborz Mountains, extending west to the Western foothills of the Zagros Mountains and encompassing the entire Khuzestan plain. Its distribution also includes all the lowlands of southern Iran, the Southern Zagros, and the coastal plains of Bushehr along the Persian Gulf coast, extending south of Jazmurian to the Makran coasts. It is also present in the southern parts of the Eastern Mountains in Baluchistan and the Zabul plain.

Genus Xerotyphlops Hedges, Marion, Lipp, Marin & Vidal, 2014.

The molecular phylogeny indicates that Xerotyphlops is an early diverging clade within Typhlopidae that appears to have originated and diversified in desert regions. Xerotyphlops vermicularis exhibits the widest distribution, with isolated and fragmented populations occurring across mediterranean and semi-arid regions in southeastern Europe, the Middle East, and north Africa. In Europe, it is found in Greece, Albania, Bulgaria, and European Turkey. These populations likely dispersed from southwest Asia. In the Middle East, its range extends from Turkey to Iran and the Arabian Peninsula, representing the core portion of its distribution. The core populations in the Middle East likely harbor the greatest genetic diversity. From here, range expansions occurred outward across North Africa and into southeastern Europe. In Africa, it occurs in coastal northwestern Africa from Morocco to Tunisia, possibly representing a range expansion from southwest Asia. The disjunct distribution between Europe, the Middle East, and Africa likely reflects range expansions during past wetter climates, followed by fragmentation as aridification intensified in the late Miocene and Pliocene [54–56].

In Iran the genus is found in the northeastern Kopet-Dagh mountains, the Gorgan Plain, and the southern Alborz Mountain slopes up to the Central Plateau’s northern borders. It also inhabits the northern Alborz Mountain slopes down to the Caspian Plain coastline, and the northwestern Azerbaijan highlands to the Moghan plain. In the Zagros Mountain range, its distribution extends north to the Central Mountains at the southern edge of the Central Plateau, and west to the rocky borders of the Khuzestan plain.

Genus Eryx Daudin, 1803.

Molecular phylogenies indicate that the genus Eryx originated in Africa and dispersed multiple times between Africa and Eurasia during the Miocene. At least three dispersal events between Africa and Eurasia occurred based on dated molecular phylogenies. The first dispersal was from Africa to Asia in the Middle Miocene, giving rise to the Asian clade. The second dispersal was from Africa to China in the Late Miocene, evidenced by the fossil E. linxiaensis which groups with the extant E. colubrinus. The third dispersal likely involved the spread of E. jaculus from Africa into Europe and Asia, though the exact timing remains uncertain. These intercontinental exchanges were likely facilitated by land bridges and aridification during the Miocene. Recent studies have revealed uncertainty regarding the taxonomic validity of E. jaculus and some related sand boa populations. The holotype in Egypt displayed morphological differences when compared to populations previously classified as this species from western Iran and Iraq. Substantial genetic divergence was also found between the Iranian and Iraqi populations. Some distinctions were noted in habitat preferences and morphological traits as well, implying that the western Asian populations potentially constitute new species separate from true E. jaculus. However, more sampling and analysis of topotypic Egyptian E. jaculus material is still required to define unambiguous species boundaries. For the time being, the western Iranian populations are provisionally labeled Eryx sp., while the Iraqi populations are designated Eryx cf. jaculus [57–59].

In Iran the genus is found in various regions of Iran, excluding the Caspian Plain and Central Plateau. Interestingly, each of the four taxa has selected one of the four corners of the country as their dominant geographical ranges.

Genus Boiga Fitzinger, 1826.

The phylogeny and biogeography of the genus Boiga indicate an Indochinese origin, with downstream dispersal events to islands and continental regions such as South Asia. The phylogeny supports Boiga as a monophyletic genus and identifies three major clades (A, B, C). Boiga trigonata is part of clade B, for which the ancestral range is reconstructed as either Indochina or Indochina+Africa. This suggests B. trigonata likely dispersed from Indochina to South Asia. No instances of reverse colonization were inferred for B. trigonata. Its presence in South Asia is consistent with the predominant downstream dispersal pattern observed in the genus [60].

The sole member of this genus in Iran is found in the semi-desert regions of the country’s eastern half. Its distribution spans from the Makran coast, around Jazmurian, to the southernmost areas of the Central Mountains. It extends northwards through the eastern regions of the Central Plateau, reaching as far as the northeastern Kopet-Dagh mountains and the Turkmen Steppe.

Genus Coronella Laurenti, 1768.

The smooth snake genus Coronella exhibits both deep evolutionary divergences dating back to the Miocene/Pliocene epoch as well as more recent post-glacial population structure, particularly in southern peninsulas like Iberia. The genus has adapted to colder and drier climates over time, influencing its current biogeography. Phylogenetic studies indicate C. austriaca and C. girondica are sister taxa that diverged in the Late Miocene/Early Pliocene period around 5–10 Mya. Mitochondrial DNA analyses reveal that C. austriaca has three major genetic lineages: Western (Iberia), Central (Central Europe and Balkans), and Eastern (Caucasus). This structure reflects historical barriers like mountains. There is a reduction in genetic diversity from south to north within each lineage, consistent with post-glacial northward expansions. Iberian populations of C. austriaca exhibit strong phylogeographic structure, with distinct clades dating back to the Messinian Salinity Crisis (~5 Mya). This suggests the Iberian Peninsula was an important long-term glacial refuge. Overall, the genus displays both ancient divergences and more recent population structure, shaped by climate change and barriers like mountains over time [61–65].

Coronella austriaca in Iran is found in the northern regions, starting from the Azarbaijan mountains and Moghan Plain. Its distribution extends eastwards along the Caspian plain and the northern slopes of the Alborz Mountain range, reaching up to the Gorgan plain.

Genus Dolichophis Gistel, 1868.

The whip snake genus Dolichophis is distributed across Europe, the Middle East, and Asia. It was previously classified within the genus Hierophis, but molecular phylogenetic studies have shown it represents a distinct evolutionary lineage. Phylogeographic analyses suggest an early divergence between European versus Middle Eastern/Asian species groups within Dolichophis. The European species form one distinct phylogenetic lineage, while the Middle East/Asia species comprise a separate closely related lineage. Biogeographically, Dolichophis likely originated and diversified within the Mediterranean region and arid zones of the Middle East and Asia. The morphological differences observed between the species groups may reflect local adaptations to their environments over time. Overall, Dolichophis exhibits phylogenetic structure consistent with an early split between European and Middle Eastern/Asian lineages, followed by localized diversification shaped by climate and geography [66, 67].

This genus is found in various regions of Iran, excluding the Central Plateau and Sistan and Baluchistan in the southeast. Two species are distributed in the northern half of Iran, spanning from the northwestern Azerbaijan Mountains and North Zagros, eastwards along the Alborz Mountain range and the Caspian plain, reaching the Gorgan plain and parts of Kopet-Dagh in northeast. The third species, endemic to the Zagros Mountains, extends from its southern slopes to the Persian Gulf coasts.

Genus Eirenis Jan, 1863.

The dwarf snake genus Eirenis represents a specialized lineage descended from Hierophis-like ancestors that dispersed and diverged within the arid regions surrounding the Mediterranean basin. Within the E. persicus complex, the divergence of the subgenus Pseudocyclophis likely occurred around 16–18 Mya, corresponding to the isolation of the Iranian plateau from the Anatolian plateau. This suggests the lineage dispersed into the Iranian plateau across the Alborz mountains. Further divergence into western and eastern clades occurred around 10–13 Mya, corresponding to the collision of the Arabia-Eurasia plates and formation of the Zagros mountains. This provided new habitats for divergence of the lineages. Diversification and speciation within the clades corresponded with mountain formation events in the Zagros, Alborz, and Himalaya ranges during the Miocene-Pliocene epoch, which formed new habitats and climatic zones. Overall, the phylogeography of Eirenis reflects an initial dispersal into the Iranian plateau, followed by divergence and speciation driven by geological events like mountain formation over the past ~20 million years [68].

The genus, boasting the highest number of species in Iran, is generally found throughout the country, with the exception of the Caspian and Gorgan plains. While some species are observed only in their type localities and others have a restricted distribution, the genus as a whole exhibit a broad presence across Iran.

Genus Elaphe Fitzinger, 1833 and Zamenis Wagler, 1830.

The genus Elaphe has a widespread distribution across the Palearctic, northern Oriental, Nearctic and northern Neotropical regions, occupying heterogeneous habitats including mountain forests, grasslands, deserts, and tropical forests. The genus likely originated in tropical Asia based on the basal position of species like E. porphyracea, suggesting an Asian origin. Elaphe dispersed from Asia to North America a single time via the Bering Land Bridge during the early Miocene, leading to the radiation of New World ratsnakes. In contrast, the genus dispersed from Asia to Europe multiple times, resulting in distinct lineages like Zamenis in Europe. However, basal Zamenis lineages are found in the Middle East (Z. hohenackeri and Z. persica) indicating east to west dispersal in the Old World. Overall, the evolutionary history of Elaphe reflects dispersal out of tropical Asia, colonization of new regions, and subsequent in situ diversification [69–71].

The genera Elaphe and Zamenis share overlapping distributions in Iran. Both are found in the northwestern Azerbaijan Mountains and the Moghan plain, extending to the Alborz Mountain range. They also inhabit the lowlands, including the Caspian and Gorgan plains. Furthermore, Zamenis extends south to the Central Zagros.

Genus Hemorrhois Boie, 1826.

The colubrid snake genus Hemorrhois is distributed across northern Africa, the Iberian Peninsula, and western Asia. Molecular phylogenetic analyses have identified two primary clades within Hemorrhois corresponding to distinct geographic ranges: A western clade comprising H. hippocrepis and H. algirus found in northwest Africa and the Iberian Peninsula, and an eastern clade containing H. ravergieri and H. nummifer in central Asia. These two clades are separated by the arid regions of North Africa, suggesting that an ancient vicariant event fragmented the ancestral distribution. From a biogeographical perspective, Hemorrhois likely originated and initially diversified within Mediterranean coastal regions. The central Asian species represent a subsequent eastward dispersal and geographic isolation event. Overall, the phylogeography of Hemorrhois reflects an evolutionary history shaped by fragmentation of an ancestral coastal range, vicariance, and long-distance dispersal [66].

The genus exhibits a broad distribution across Iran, inhabiting various habitats. However, it has yet to be recorded in certain regions, including the Persian Gulf coast stretching from the Khuzestan Plain to Makran and the Jazmurian Basin, as well as the Lut Desert and the central areas of the Central Desert.

Genus Lycodon H. Boie in Fitzinger, 1826.

The colubrid snake genus Lycodon has a broad distribution across South and Southeast Asia, ranging from India and Sri Lanka eastwards to southern China and Southeast Asia. The L. aulicus species group occurs in South Asia, including India, Sri Lanka, and parts of Central Asia. This group contains L. striatus and related species, and is thought to have originated in Southeast Asia based on the basal position of L. jara from Myanmar. Biogeographically, members of this group likely dispersed westwards along the Himalayan foothills into Central Asia and southwards into peninsular India and Sri Lanka. The L. striatus complex refers to a subgroup of similar-looking barred and striped species including L. striatus, L. bicolor, and related taxa. Molecular phylogenies reveal two main lineages within the L. striatus complex: L. striatus sensu stricto, distributed in eastern and central India and Sri Lanka, and L. bicolor occurring in Central Asia and Pakistan. L. striatus likely dispersed from mainland Asia into Sri Lanka during Pleistocene glacial periods when sea levels were lower, supported by the shallow genetic divergence between Indian and Sri Lankan populations. In contrast, L. bicolor originated in Southeast Asia and dispersed westwards into Central Asia, following river valleys and plains. It exhibits a pattern of clinal variation in coloration along elevation gradients. The two lineages abut but do not significantly overlap in northwestern India, with the Indus River potentially forming a barrier between them. Overall, the biogeography of Lycodon reflects an evolutionary history of dispersal, isolation, and diversification across South and Southeast Asia [72].

The sole member of this genus in Iran, L. bicolor, exhibits two distinct distributions in eastern Iran. In the southeast, it is found in the Zabol plain and the foothills of the Eastern Mountains in Sistan and Baluchistan. In contrast, its northeastern distribution includes the northeastern Kopet-Dagh Mountains, extending westward to the Gorgan plain.

Genus Lytorhynchus Peters, 1863.

The colubrid snake genus Lytorhynchus consists of small, fossorial species inhabiting arid regions of Africa, the Middle East, and southwestern Asia. This genus likely originated in Arabia or northeast Africa, later dispersing into Southwest Asia. The species of Lytorhynchus have allopatric distributions, suggesting isolation in different arid zones permitted divergence. Overall, the biogeography of Lytorhynchus reflects an evolutionary history of origin in Africa/Arabia, dispersal into Southwest Asia, and allopatric speciation driven by isolation across arid habitats [66, 67].

Excluding two species that are confined to the southwest and southeast, the third species of this genus is widely distributed across Iran. However, it is notably absent from the highlands of the Alborz and Zagros Mountains, the northwestern Azarbaijan Mountains, and the Caspian Plain.

Genus Oligodon Blyth, 1860.

The colubrid snake genus Oligodon is primarily distributed across tropical South and Southeast Asia, however two species extend into the Middle East and Central Asia: O. russelius and O. taeniolatus. The O. taeniolatus populations in Iran and Turkmenistan are genetically and morphologically distinct, representing a separate evolutionary lineage called O. transcaspicus restricted to the Kopet-Dagh Mountains. In contrast, O. russelius occurs further east in Pakistan and Afghanistan. O. transcaspicus likely diverged earlier in the Miocene or Pliocene compared to O. russelius, which exhibits less differentiation across South Asia. The high Hindu Kush Mountains and arid Central Asian deserts probably impeded east-west dispersal and range expansion. Suitable habitats like semi-arid shrublands may have facilitated dispersal during certain Plio-Pleistocene climate periods. Both species represent important biogeographic components in the otherwise Palearctic Middle and Central Asian herpetofauna. Their disjoint modern distributions reflect past climate fluctuations and geological changes impacting connectivity between South and Central Asia [73].

The sole representative of this genus in Iran inhabits specifically the northern edges of the northeastern Kopet-Dagh Mountains, and the Turkmen Steppe.

Genus Persiophis Rajabizadeh, Pyron, Nazarov, Poyarkov, Adriaens & Herrel 2020.

The monotypic genus Persiophis contains the single species Persiophis fahimii, which is endemic to southern Iran. Molecular phylogenetic analyses place Persiophis in a clade with other colubrid genera found in southwestern Asia, including Rhynchocalamus and Lytorhynchus. Persiophis likely represents a relictual eastern lineage that is adapted to the arid mountains of Iran. The origin of Persiophis remains uncertain, but likely involves the isolation of an ancestral population within Iran’s extensive central mountain ranges at some point in the past 20 Mya. Persiophis may represent an ancient divergence in the region, or could reflect more recent dispersal from adjacent desert regions. Further research is needed to elucidate the evolutionary history and biogeography of this enigmatic snake lineage [67].

Genus Platyceps Blyth, 1860.

The colubrid snake genus Platyceps is distributed across SE Europe, northern Africa, the Middle East, and western and central Asia. Molecular phylogenetic studies support Platyceps as a monophyletic genus. Within Platyceps, some phylogenetic structure corresponds to geographic distributions: P. atayevi and P. najadum from Armenia and SE Europe and western Asia respectively, form one clade, while P. florulentus and P. rubriceps from the Middle East form another. P. karelini and P. rogersi from western Asia are sister taxa, and P. rhodorachis from Turkmenistan occupies a basal position relative to the other species. This pattern suggests an early divergence between central Asian and Middle Eastern Platyceps species groups. Biogeographically, Platyceps likely originated in the arid regions of central Asia, later dispersing and diversifying into the Middle East. The phylogenetic proximity of central Asian species reflects their shared biogeographic history, while Middle Eastern species also share a close evolutionary relationship, having diversified within that region. Further phylogenetic and phylogeographic analyses within Platyceps could elucidate the timing and nature of diversification within this widespread genus [66, 67]. Members of this genus exhibit a widespread distribution across the entirety of Iran.

Genus Rhynchocalamus Günther, 1864.

The snake genus Rhynchocalamus comprises small, secretive species endemic to the Middle East region. Phylogenetic and biogeographic evidence suggests the genus likely originated in the Levant, followed by range fragmentation leading to the current disjunct distribution pattern. Each species occupies a distinct geographic range separated by expansive desert habitats, likely due to niche constraints restricting them to rocky slopes and precluding dispersal across sandy deserts. The Miocene expansion of arid habitats in Arabia and North Africa probably caused vicariance events that isolated ancestral populations. Molecular dating estimates that the genus diverged from its sister clade Lytorhynchus around 26 Mya (Late Oligocene). Within Rhynchocalamus, initial diversification began in the Middle Miocene with the northern lineage R. satunini diverging approximately 15 Mya. Further speciation occurred in the Middle Miocene, separating R. arabicus and R. dayanae (formerly R. melanocephalus) around 9 Mya. R. melanocephalus diverged around 11 Mya and underwent additional radiation in the Pliocene around 3.5 Mya. Ongoing tectonic activity and marine barriers in the Middle East from the Oligocene onwards drove vicariance and allopatric divergence of these geographically isolated species. Quaternary climate changes causing expanding arid zones likely restricted species ranges to their current fragmented distributions [74–77].

The distribution of this genus in Iran is discrete, with records indicating its presence in isolated locations such as the northwestern Azarbaijan Mountains and the southern slopes of the Central Alborz Mountains. Nevertheless, its dominant distribution is concentrated in the Zagros Mountains, particularly the western foothills of the Zagros Mountains.

Genus Spalerosophis Jan, 1865.

The colubrid snake genus Spalerosophis has a disjunct Saharo-Sindian distribution across arid regions of Afro-Arabia, the Irano-Turan region, and Indo-Pakistan. Phylogenetic analyses indicate the earliest diverging lineage is S. microlepis endemic to the Zagros Mountains of Iran, dating back to the early Miocene around 21.7 Mya. This suggests an Iranian Plateau origin for the genus. Subsequent cladogenic events coincided with major geological uplifts that likely drove vicariance and allopatric speciation. The Zagros Mountains separated western (S. diadema cliffordii) and eastern (S. diadema schirasianus) lineages approximately 16.7 Mya based on a substantial phylogenetic split, supporting their status as distinct species. Further east, the Sulaiman Mountains uplift segregated S. arenarius and S. atriceps around 13.3 Mya from ancestral populations in Afghanistan and Pakistan. These sister taxa diverged more recently during the late Miocene, around 7.9 Mya. The restricted range of S. microlepis in the Zagros highlands is attributed to isolation by surrounding inhospitable lowland deserts. In summary, the evolutionary history of Spalerosophis reveals a predominant role of mountain barrier formation and regional vicariance events across the Middle East in shaping biogeographic patterns and phylogeographic structure from an Iranian Plateau origin [78].

The distribution of this genus is widespread across Iran, with the exception of the Caspian plain and the northwestern Azarbaijan Mountains.

Genus Telescopus Wagler, 1830.

The genus Telescopus likely originated in Africa based on phylogenetic analyses, with its distribution centered in arid regions across Africa, Arabia, the Levant, southeastern Europe, and western Asia. Two main dispersal events out of Africa occurred: one to Arabia in the Miocene, and another across the Tethys Sea to southeastern Europe/western Asia around the Oligocene-Miocene boundary. Phylogenetically, there is a deep split between a northern clade (T. fallax, T. hoogstraali, T. nigriceps) and the remaining southern, Afro-Arabian species. Diversification of the genus does not appear to be constrained by climatic niche conservatism, as there is no clear phylogenetic signal related to climatic niche characteristics. Overall, the current distribution of Telescopus reflects an initial African origin followed by two major dispersal events out of the continent along arid corridors, with climatic niches evolving flexibly during diversification [60, 79, 80]. Members of this genus exhibit a widespread distribution across the entire Iran.

Genus Natrix Laurenti, 1768.

Phylogenetic and phylogeographic studies show that the semiaquatic snake genus Natrix likely originated in the Late Miocene around the Mediterranean region and subsequently dispersed outward. For N. tessellata, the oldest lineages originated in southwest Asia, particularly Iran, in the Miocene. From this origin, it spread both westward (reaching the eastern Mediterranean, Balkans, and Central Europe) and eastward into Central Asia, dispersing along major river valleys and basins. Postglacial warming allowed northward expansions in Central Asia following river valleys into steppe habitats. In contrast, N. natrix originated around the Mediterranean and expanded outward after the last glacial maximum from southern refugia like the Balkans and Italy. Lineages spread across northern Europe as well as into central Europe, with additional colonization of northeastern Europe from the Caucasus and Fennoscandia from southern and eastern refugia. Range expansions followed postglacial warming and melting ice sheets, with secondary contact between lineages. Dispersal ability in Natrix is facilitated by utilization of aquatic habitats, but distributions are limited by dry regions, high elevations, and cold areas. Overall, phylogeographic patterns in Natrix reflect Miocene origins around the Mediterranean, range expansions from southern refugia after glacial retreats, and dispersal along river valleys and shorelines [81–85].

The genus has a widespread distribution in Iran. It inhabits all mountain ranges, including the northeastern Kopet-Dagh Mountains, both the northern and southern slopes of the Alborz Mountains, the northwestern Azerbaijan Mountains and the Moghan steppe, and extensive parts of the Zagros Mountains, excluding the southern slopes. Furthermore, its distribution encompasses the northern Caspian and Gorgan plains, as well as specific habitats within the Khuzestan plains.

Family Psammophiidae Bonaparte, 1845.

The psammophiine snakes comprise one of the major early-diverging clades within Lamprophiidae. Molecular phylogenetic analyses reveal two primary clades: one containing the northern African and Eurasian genera Malpolon and Rhamphiophis, and another with the remaining sub-Saharan genera such as Mimophis, Hemirhagerrhis, and Psammophis. The basal position of Malpolon and Rhamphiophis suggests an ancestral distribution centered in northern Africa and west Asia for early psammophiine lineages, with subsequent diversification across sub-Saharan Africa. Phylogeographic structure corresponding to geographic barriers like the Great Rift Valley in sub-Saharan genera indicates allopatric divergence has played a role in diversification [86, 87].

Genus Malpolon Fitzinger, 1826.

The genus Malpolon likely originated in Africa, potentially the Maghreb region of northern Africa, based on its inclusion within the largely African psammophiine clade and sister relationship with the monotypic genus Rhagerhis moilensis. Divergence dating estimates the initial split within Malpolon at 3.5–6 Mya between western and eastern African clades. From the Maghreb, Malpolon dispersed west into southwest Europe and east around the Mediterranean. The western clade M. monspessulanus appears to have invaded southwest Europe across the Strait of Gibraltar during the Pleistocene, while the eastern M. insignitus clade spread earlier over a prolonged period around the eastern Mediterranean and into southwest Asia, acquiring greater genetic diversity. Fossil evidence indicates an earlier Pliocene invasion of southwest Europe by Malpolon, later replaced by recent arrivals. Overall, Malpolon exhibits a pattern of dispersal out of Africa, with the Strait of Gibraltar periodically facilitating migration between Africa and Europe. Divergence dating suggests M. insignitus split from its sister species M. monspessulanus around 4.6–8 Mya, with significant genetic divergence supporting its probable status as a distinct genus adapted to more arid conditions [88–91].

The genus Malpolon is represented in Iran by a single species, which exhibits a wide distribution across various regions. Its range encompasses the northwestern Azerbaijan Mountains and Moghan Plain, extends along the southern slopes of the Alborz Mountain range, and reaches eastward to the northeastern Kopet-Dagh Mountains. This taxon is also prevalent throughout the majority of the Zagros Mountain range, spanning from the northern slopes proximal to the Central Mountains to the southern slopes abutting the Persian Gulf. Notably, this species has not been documented within the Khuzestan Plain. Conversely, the genus Rhagerhis exhibits a primary distribution within the Khuzestan plain. Its range extends to the easternmost boundaries of the Persian Gulf coasts, yet does not extend further eastward, with no documented sightings along the Makran coasts.

Genus Psammophis Boie, 1826.

Within Africa, Psammophis exhibits substantial phylogeographic structure and genetic divergence between populations isolated in different refugia during past climate shifts. Diversification likely began in the Late Miocene-Pliocene, driven by aridification and fragmentation of mesic habitats. Geographic barriers like the Atlas Mountains and river valleys have also restricted gene flow, promoting divergence. In Asia, deep genetic divergence between P. lineolatus and P. turpanensis likely resulted from uplift of the Tian Shan Mountains ~6 Mya. Broad distributions of some species indicate use of dispersal corridors like river drainages to traverse barriers during mesic periods [92–95].

The genus is widely distributed across Iran, with the exception of the northern and northwestern regions. These excluded regions encompass the Caspian plain, the northwestern Azerbaijan Mountains, the Moghan plain, parts of the northern Zagros, and the northern slopes of both the Central and Western Alborz mountains.

Genus Bungarus Daudin, 1803.

The genus Bungarus originated in Asia and contains around 15 species of kraits. The center of diversity is in tropical southern Asia, with the highest species richness in India and Southeast Asia. Bungarus likely diverged from other elapid snakes around 25–30 Mya during the Oligocene epoch. Several studies using mitochondrial DNA sequences have revealed cryptic diversity and uncovered independently evolving lineages within wide-ranging Bungarus species: Three major clades were found within B. fasciatus corresponding to Indo-Myanmar, Sundaic, and East Asian distributions. Three phylogenetic lineages are recognized within the B. multicinctus complex in Southeast Asia and southern China, elevating them to full species status: B. multicinctus, B. candidus, and B. wanghaotingi. Deep genetic divergences suggest additional cryptic diversity likely remains to be characterized within the B. multicinctus complex. B. sindanus shows divergence between northern (Pakistan, northern India, Nepal) and southern (peninsular India) lineages, estimated to have split around 6 Mya. Biogeographic barriers such as the Isthmus of Kra in Thailand have influenced the evolutionary differentiation between mainland and Sundaic (island Southeast Asian) populations. Cycles of connection and fragmentation of landmasses caused by sea level fluctuations (e.g., the Sunda shelf) during the Pleistocene epoch have shaped phylogeographic patterns within Bungarus. Drier climatic conditions forming barriers to dispersal (e.g., in central India) led to divergence between northern and southern lineages within B. caeruleus, B. sindanus, and possibly other species. Overall, the evolutionary relationships and taxonomy of Bungarus remain incompletely resolved. Integrative approaches combining morphological, ecological, and expanded molecular data will help clarify species boundaries and diversification processes within this medically significant snake genus [96–100].

The distribution of this genus extends westward, with its westernmost boundary reaching the coast of Makran in the southeast of Iran.

Genus Naja Laurenti, 1768.

The genus Naja originated in Africa and consists of 4 subgenera: Naja, Uraeus, Boulengerina, and Afronaja. The typical subgenus Naja likely originated from a single invasion of Asia from Africa. N. oxiana has a western Asian distribution in the Trans-Caspian region across northeastern Iran, Turkmenistan, Uzbekistan, Tajikistan, Afghanistan, Pakistan, and northern India. Phylogenetically, N. oxiana forms a clade with other central/western Asian cobras: N. kaouthia, N. sagittifera, and N. atra. This suggests a relatively rapid expansion of Naja from eastern to western Asia. Within its Trans-Caspian range, N. oxiana does not show clear genetic differentiation or subdivision. This suggests rapid dispersal from eastern Iran westwards without major barriers, allowing panmixia. The divergence of N. oxiana from N. kaouthia/N. sagittifera was estimated around 3.2 Mya in the late Pliocene. This corresponds with the spread of more open, arid habitats in Asia, allowing westward expansion. Demographic analyses indicate N. oxiana underwent population expansion around 2 Kya in the late Holocene, likely facilitated by its range in open foothill habitats not impacted by Pleistocene glaciations [101–103].

The genus has a distribution in Iran that spans from the Eastern Mountains, located east of the Central Plateau, to the Gorgan City. Its range extends along the northeastern Kopet-Dagh Mountains and reaches the Eastern Alborz Mountains and Turkmen steppe.

Genus Walterinnesia Lataste, 1887.

Phylogenetic analysis shows that Walterinnesia forms a monophyletic group within the cobra family Elapidae, based on mitochondrial DNA sequences. This supports Walterinnesia as a distinct evolutionary lineage. Within Walterinnesia, W. aegyptia and W. morgani are very closely related sister taxa. The genetic divergence between them is extremely small based on mitochondrial DNA. W. morgani was originally described from Iran, suggesting an eastward distribution, distinct from W. aegyptia in Africa/Arabia. However, the Saudi Arabian specimens identified genetically as W. morgani are virtually identical to W. aegyptia, indicating they are the same species. This suggests the biogeographic boundary between W. aegyptia and W. morgani may break down, and they should be treated as conspecific with a broad Middle Eastern/North African distribution. More sampling and genetic analysis is needed to confirm the range limits and evolutionary relationships between various populations currently assigned to W. aegyptia or W. morgani across the region. The broad distribution of W. aegyptia reflects the desert/arid-adapted ecology of the species, allowing it to span Northern Africa and the Arabian Peninsula [104].

The distribution of desert cobra in Iran begins from the western foothills of the Zagros Mountains and the Khuzestan plain. It extends along the southern slopes of the Zagros Mountains and the coasts of the Persian Gulf, reaching as far as the northwestern regions of the Jazmurian depression located in southern Kerman Province.

Genus Gloydius Hoge & Romano-Hoge, 1981.

The genus Gloydius (Asian pit vipers) has a broad distribution across northern Asia, ranging from Europe in the west to China in the east. Phylogenetic analyses indicate that during the Pleistocene glacial periods, Gloydius populations expanded out of the eastern Palearctic region towards more central areas and lower latitudes, tracking cooler climates. One member of this genus, G. caucasicus, is distributed across northeastern to northwestern Iran and southern Azerbaijan. Dated phylogenetic trees indicate that G. caucasicus diverged from its sister species G. caraganus around 1.89 Mya in the early Pleistocene. Further diversification within G. caucasicus itself initiated in the mid-Pleistocene, starting approximately 1.25 Mya. This resulted in four primary mitochondrial lineages that are spatially distributed from northeastern to northwestern Iran. The divergence of these lineages was likely driven by cooling climates and glacial cycles during the Pleistocene, which restricted gene flow among populations leading to allopatric fragmentation. Their geographic distributions suggest isolation in multiple refugia along the Alborz Mountains. Phylogeographic analyses support the hypothesis that G. caucasicus dispersed from northeastern Iran westwards via the northern and southern slopes of the Alborz Mountains [52, 105].

The distribution of this genus extends westward, with its westernmost boundary reaching eastern Caspian Sea. This genus, represented by one species, spans the northern part of the Iran. It covers both low-altitude lands, including the Gorgan and Caspian plains, and the northeastern Kopet-Dagh Mountain ranges, as well as the Turkmen steppe. The distribution encompasses the entire Alborz Mountain range, including the northern and southern slopes, and extends to the Talesh Mountains, which mark the westernmost limit of its range.

Genus Cerastes Laurenti, 1768.

The horned vipers of the genus Cerastes are distributed across northern Africa, the Sinai Peninsula, the Arabian Peninsula, and parts of the Middle East. Recent genomic evidence reveals an unexpected phylogenomic relationship within Cerastes, with C. cerastes and C. vipera recovered as sister species while C. gasperettii is more distantly related. This suggests C. cerastes likely originated in Africa, with later dispersal of an ancestral lineage into Arabia around 7 ± 3.83 Mya following increasing aridity during the late Miocene. Subsequent isolation and speciation of this Arabian lineage gave rise to C. gasperettii. Plio-Pleistocene climatic fluctuations around 4.22 ± 2.23 Mya then caused geographic isolation and speciation of the African ancestor into the current C. cerastes and the sand-specialist C. vipera. Within C. cerastes, genetic differentiation distinguishes several intraspecific lineages: northwestern African C. c. cerastes, northeastern African C. c. cerastes (Chad, Egypt), and Arabian C. c. hoofieni dated around 1.70 ± 0.92 Mya. For C. gasperettii, phylogeographic structure separates northern (Iran, eastern Arabia) and southern (Yemen, Oman) clades. However, relationships within C. gasperettii are not fully resolved due to limited sampling. Overall, the biogeographic pattern suggests an older African C. cerastes lineage that later dispersed into Arabia, isolating C. gasperettii. Subsequent aridification facilitated C. gasperettii’s rapid range expansion, while geographic barriers (e.g. Red Sea) and climatic shifts likely drove vicariance and divergence within C. cerastes. Secondary contact between divergent lineages probably occurred during range expansions [106–110].

A single species of this genus exhibits a restricted distribution, confined to the Khuzestan plain, southwestern Iran.

Genus Echis Merrem, 1820.

The saw-scaled vipers of the genus Echis exhibit a widespread distribution across Africa, Arabia, and South/Southwest Asia. Phylogenetic analyses have revealed four main clades within Echis that largely correspond to geographic regions: the E. ocellatus group in West Africa; the E. pyramidum group in Africa north of the equator and Arabia; the E. coloratus group in Arabia; and the E. carinatus group in Southwest and South Asia. This disjunct distribution reflects the complex biogeographic history of Africa and Eurasia colliding in the early Miocene, followed by vicariance events like the opening of the Red Sea. Genetic divergence between the main clades generally reflects their geographic separation. The West African E. ocellatus group is the most divergent, indicating a long history of isolation. Within the E. pyramidum group, African and Arabian populations form deeply divergent sister clades, likely due to vicariance from the late Miocene opening of the Red Sea. Arabian members of this group show further subdivision, with divergence between E. khosatzkii in Oman and other taxa in Yemen. The Arabian E. coloratus group contains the closely related but deeply divergent taxa E. coloratus and E. omanensis, separated by arid lowlands in Eastern Arabia. In contrast, the broad-ranging E. carinatus group of South/Southwest Asia exhibits very low genetic divergence, suggesting rapid and recent dispersal northward from an origin in southern India. Populations across the northern part of the E. carinatus range (Pakistan, Iran, Middle East) are almost identical, while more divergent haplotypes originate from southern India. This points to a range expansion northward into southwest Asia likely occurring in the late Pliocene or Pleistocene [107, 109–112].

This genus has an extensive distribution in Iran. It is found in the northeastern Kopet-Dagh Mountains (excluding the Turkmen steppe), the Central Plateau, and the Central Mountain. Its range also covers Sistan and Baluchistan, Makran, and the coasts of the Persian Gulf extending to the Khuzestan Plain. Additionally, this genus is distributed throughout the Zagros Mountains, with the exception of the extremely cold heights of the Central Zagros.

Genus Macrovipera Reuss, 1927.

The viper genus Macrovipera is distributed across North Africa, the eastern Mediterranean islands, the Levant, and eastwards into Asia as far as Kashmir. The center of diversity is in Asia, where species inhabit foothill, mountain, semi-desert, and steppe habitats. Tree species are widely recognized, M. lebetina, M. razii and the range-restricted M. schweizeri of the western Cyclades islands (Greece). M. lebetina is the predominant Macrovipera species in Asia and has several described subspecies across its range. Phylogenetic analysis of Iranian Macrovipera using the cytochrome b gene revealed two major clades: Clade A represents M. razii, endemic to Zagros Mountains. Clade B comprises two subclades—B1 in western/northwestern Azarbaijan and Alborz Mountains (M. l. obtusa) and B2 in northeastern Kopet-Dagh Mountains (M. l. chernovi). The divergence of M. razii around 10.5 Mya coincided with Zagros Mountains uplift. M. l. obtusa shows high haplotype diversity, suggesting persistence in northwestern Iran during Pleistocene glacial-interglacial cycles, characteristic of a glacial refuge. The discovery of the Iranian endemic M. razii highlights the role of geological and climatic events in shaping Macrovipera biogeography and phylogeography. Further research is still needed to fully elucidate the evolutionary history of this genus [109, 110, 113].

Genus Montivipera Nilson, Tuniyev, Andrén, Orlov, Joger & Herrmann, 1999.

The viper genus Montivipera is endemic to mountainous regions of the Near and Middle East, distributed from eastern Greece, western Turkey, Lebanon, Syria and Armenia to central Iran. This genus contains several rare and endangered species with small, isolated populations. Phylogenetic analyses indicate Montivipera diverged from Macrovipera around 12–15 Mya during the Miocene, coinciding with Anatolian-Iranian plateau uplift and formation of the mountain chains they now inhabit. Two major clades are recognized: the xanthina complex in western Anatolia and the Levant, and the raddei complex in eastern Anatolia, the Caucasus, and Iran. These likely diverged due to tectonic movements separating populations. Diversification and speciation within Montivipera occurred mainly in the Pliocene and Pleistocene, driven by climatic oscillations that caused range fragmentation and isolation in montane refugia, resulting in allopatric divergence. Distribution modeling shows Montivipera habitats have shifted to higher elevations since the Last Glacial Maximum around 21,000 years ago, indicating climate change has been a major influence. Suitable habitats are now highly fragmented and isolated on mountaintops, containing genetically distinct populations. Many unknown isolated populations likely exist. Phylogeographic patterns show association with historical plant refugia in regional mountains, suggesting common effects of past climate changes [114–117].

The members of this genus in Iran exhibit a restricted distribution, confined to the highlands of the Alborz Mountains, the northwestern Azerbaijan Mountains, and the Central Zagros Mountains.

Genus Pseudocerastes Boulenger, 1896 and Eristicophis Alcock & Finn, 1896.

Pseudocerastes and Eristicophis likely originated in the Arabian Peninsula. Ancestral populations were probably located in western Arabia, as the basal mitochondrial and nuclear gene lineages are found in P. fieldi from Israel, Syria and Iraq. Biogeographic reconstructions suggest an eastward dispersal of these genera from western Arabia onto the Iranian Plateau around 12–13 Mya (Miocene). This coincides with the formation of the Gomphotherium land bridge which likely facilitated trans-Arabian dispersal. The genus Eristicophis is currently restricted to the Registan–North Pakistan sandy desert, implying an isolation and speciation event in this eastern region. Within Pseudocerastes, P. persicus and P. urarachnoides likely diverged around 8 Mya (Miocene), potentially driven by the uplift of the Zagros Mountains acting as a vicariant barrier. Further lineage diversifications occurred more recently during the Pliocene and Pleistocene. Phylogeographic patterns reveal subdivision into an Arabian P. fieldi group and a Zagros/Iranian Plateau P. persicus/P. urarachnoides group, with isolation of populations by historical events like mountain uplift and climatic oscillations [118, 119].

Genus Pseudocerastes has an extensive distribution in Iran. It is found in the northeastern Kopet-Dagh Mountains (excluding the Turkmen steppe), the Central Plateau, and the Central Mountain. Its range also covers Sistan and Baluchistan, Makran, and the coasts of the Persian Gulf extending to the Khuzestan Plain. Additionally, this genus is distributed throughout the Zagros, with the exception of the extremely cold heights of the Central Zagros.

Genus Vipera Laurenti, 1768.

Phylogeographic studies reveal Pleistocene climatic oscillations strongly shaped genetic diversity and distribution patterns within the genus Vipera. During cold glacial periods, cold-adapted species of the subgenus Pelias expanded their ranges, while warm-adapted species became isolated in Mediterranean peninsulas. This pattern reversed during warmer interglacial periods, leading to divergence between populations isolated in different refugia (e.g. Iberia, Italy, Balkans). Several contact zones likely represent secondary contact of formerly isolated lineages. However, climatic adaptations alone do not explain all phylogeographic patterns. Topography, habitat availability, and geographic barriers also play key roles. Some species show complex patterns, and there is evidence for local climatic adaptation driving genetic divergence in certain cases, with closely related species or lineages often occupying partially or fully distinct climatic niches. V. eriwanensis is part of the ’renardi clade’, distributed in the Caucasus region and areas north/east of the Black Sea. Within this clade, V. eriwanensis forms a subclade with V. ebneri that diverged around 1.4 Mya. V. ebneri from northern Iran is probably just a subspecies of V. eriwanensis. V. eriwanensis occurs in Armenia, Nakhichevan, and northwestern Iran, inhabiting rocky habitats at moderate elevations. Recent genetic studies have found low divergence between V. eriwanensis and V. renardi, questioning its status as a distinct species. However, V. eriwanensis does show some private haplotypes in nuclear DNA and seems geographically isolated from V. renardi, and its status as a valid species is still accepted by many. Phylogeographic patterns suggest the Caucasus was an important Pleistocene refugia for V. eriwanensis and relatives, with range expansions during glacial periods [115, 120–122].

In Iran, the only species of this genus demonstrates a restricted distribution, showing a preference for the alpine steppe habitats found specifically within the highlands of the Alborz Mountains and the northwestern Azerbaijan Mountains.